A bioinformatic murder mystery

Today's Werkcollege is going to be... a bit different. Today, you are going to assume the identity of a Forensic Bioinformatician, Jamie Bits, to try and solve a murder case in a small village. For this purpose, you will get pieces of evidence, which you have to analyze with bioinformatic means. When you are moving through the story, ''don't use the undo arrows on the top left of the page unless there is no other way to leave the page''. This is important, because otherwise, ''the game will not register that you have visited the page''. Visiting certain pages will trigger your ability to find new evidence or change some of the witness statements, so ''make sure to always scroll to the bottom of the page and use the links there''. If there is no link back, then the page is definitely not a trigger page and you can use the undo arrow. When you are going through the story, remember that a real case would of course be more complicated. Our "evidence" consists of small DNA pieces and single genes, where usually longer processes are required to extract information. The methods themselves are conceptually similar to the ones that forensic scientists would use, however, in a real case, there would be a lot more statistics. I hope you have fun! [[Start->Discovery Site]]

##Discovery Site <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/discovery_site.webp'> (align:"<==>")+(box:"XXXXXXX===")["Detective Bits! Thank God you're here! The victim's ID says his name is Chris Howell, 29." The rookie looks a little green, as if he is about to throw up. "First time?", you ask him. He nods, nervoursly. You look around the parking lot. "Did you clear the area?" The rookie nods again. "The culprit is gone. The body is already cold, too. Must have been a while." "Cause of death?", you ask. "Can't say anything for sure until the medical examiner is here. The victim has a pretty big head wound though." You examine the body more closely. Indeed, the head wound is the only visible injury on the victim. You look around the body. "So, where's the blood?" The rookie looks at you, confused. "The blood? If the culprit hit the victim over the head here, this wound would have bled like crazy. Did you find any blood?" The rookie shakes is head. "No blood anywhere in the garage or on any of the cars." "Then, he wasn't killed here."] What would you like to do? [[Search the parking garage->Search the garage]] [[Examine the body->The body]] [[Give up->Give up]] (set:$soil_profiles_solved to false) (set:$crime_scene_found to false) (set:$not_your_father to false) (set:$white_material_analyzed to false) (set:$saliva_identified to false) (set:$saliva_ethnicity to false)

## Searching the garage <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/search_garage.jpg' width=612> You find some hairs around the garage. You don't find any blood. What do you do? [[Examine the hairs->examine hairs garage]] (link-undo:"Go back to the discovery site")

##Examine the body <image src="https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/body-outline.png" width=612> You examine the body thoroughly and find the following biological materials: * Saliva on the victim's cheek * A few cat hairs in the victim's coat * Traces of white biological material in the victim's pocket * Pollen or spores on the victim's coat * Mud on the victim's shoes What do you want to do? [[Go to the Lab->Forensic Lab]] [[Go to the Police station->Police Station]]

If you want to end the game, just close the tab of your browser. (link-undo:"Go back to discovery site")

## Examine the hairs from the garage <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/hair_sample.jpg' width=612> Upon closer inspection, you realize that the hairs are * All different colors * All different lengths * All without roots and therefore not suitable for DNA testing It looks like the hairs have nothing to do with the murder after all... [[Go back to the discovery site->Discovery Site]]

##Forensic Lab At the Forensic Lab, you can examine your evidence. If you want to talk to witnesses or your Captain, you will find them at the Police station. If you need instructions on how to examine your evidence, links to instructions will appear on the methods page, once you have found them. If you collect any DNA profiles, you can find and compare them under "DNA profiles". <img src="https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/forensic_lab.jpg" width=612> Your next steps: (if:(history: where its name contains "Victim Spores")'s length is 0)[* Figure out what the pollen/spores on the victim's coat are](if:$white_material_analyzed is false)[* Figure out what the white material is](if:$saliva_identified is false)[* Find out who the saliva belongs to](if:$soil_profiles_solved is false)[* Locate potential crime scenes](if:$crime_scene_found is false)[* Find the actual crime scene](if:$crime_scene_found is true and $blood_not_victims is false)[* Find out whether the blood from the bottleneck belongs to your victim](if:$not_your_father is true and $double_check is not true)[* Double-check using the sry-genes whether Chris is Theodore Howell's biological son](if:$not_your_father is true and $double_check is true and $stephen_is_the_father is not true)[* Find out who the victim's biological father is](if:$not_your_father is true and $yes_your_sister is not true)[* Find out whether Chris and Melissa are siblings through their mother's side](if:$crime_scene_found is true and $blood_not_victims is true)[* Find out who the blood belongs to and find your culprit] [[Go to the Police station->Police Station]] [[Methods for analyzing your evidence->Methods]] [[DNA Profiles->STR Profiles]] [[Examine the saliva->Victim Saliva on Cheek]] [[Examine the cat hairs->Victim Cat hair]] [[Examine the white material->Victim White material]] [[Examine the pollen/spores->Victim Spores]] [[Examine the mud->Victim Mud]] (if:$crime_scene_found is true)[[[Examine the blood evidence->Blood evidence]]]

##Evidence: Saliva on the victim's cheek You extract the DNA from the saliva you found on the victim's cheek. You gain the following evidence. See below to look at the evidence. * An 8-loci Short-Tandem-Repeat profile * A SNP profile for ethnicity identification * An SRY-Gene (unless:$saliva_ethnicity is true)[[[Instructions for determining the ethnicity of the DNA sample->Instructions ethnicity]](set:$ethnicity_instructions to true) Which region is this sample from? (dropdown: bind $saliva_region,"Choose region...", "africa","america","east asia","europe","oceania") [[Check Ethnicity->Saliva Ethnicity]]](if:$saliva_ethnicity is true and $ralph_benson_str is true and $saliva_identified is not true)[You can compare any DNA profiles you have to the saliva in [[DNA profiles->STR Profiles]]](if:$saliva_identified is true)[The saliva on the victim's cheek belongs to his partner, Ralph Benson. Does that also mean that the victim's partner is the killer?] [[Go back to the lab->Forensic Lab]] ####8-loci Short-Tandem-Repeat Profile <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/evidence_saliva.png', width=150> ####SNP profile for ethnicity identification >`SNP_profile_saliva_victims_cheek` TTGGCCAACCTTCCAAAGGGCCGGTCGAAAAGAATTTGCTGACCCTAACCACACGGTCCGCCGGCTGA ####SRY gene >`SRY_gene_saliva_victims_cheek` TGACCTTCATTTTATGGAGAGAAACAAGCTATAACATGTAGTATCTAAGCTGATTAGAAGAACTAAAAAGAGA AGCTCATACTTGTGCATCAGAAGGTAAATGAAAGAGTGAAGTTACCTCTTTGTTTTAAGGAAGAAAGGAAAAT TGTGGATGTCATCTGTTTTCTGTTTACATATTTCAGGCACGGATAGCCACAATGTGATTTTAAGACGGTTAGT TACAACTGATTTGAAAAAAAAAAAAAATGCTTCACTCTATGAGAAATTTCTTCCCAAGTATGAAACCTTGTTT TTACAGGCAATTTCCTATACTTTGAAAAAATCAAAATAATAAAGTAAAAGAAAAATAATTCAGGTGAAGTTAG AGAAAAAAACAGGCAGCATTATTTTAAAGTTGTAAACTATTTTGTTTACTTAAAGTTTAATTTACATGTAGTA GATATGCATTTGTAAGGTTCTTCGGCTCAGGTAGGAGAGCATTCTTTTTCCCACTGCACCCTACTTCATCCTC CCACTGGCAAATAATTAGATTATCCCTGGAAAAAAAAGATGCCAGTAAAATTGATCATGTTTAAATGCATCAG TTGCTAGGTGATTTATCTGATTAAGTCTTGAAACAGTAGAACCTAGCAATTAAAGTGAGCATTAACTTCTACC TACCAAATCAGAAGACTATTCTAACTTTTTGAGAATTAGATGTTGAAAATATGGCCCATGAATTTAGCTTGGT TAAAATAAAAAACATGCAAACAAAACAAACCCAACATCTTGAAAGGACATTTGACTCTAAAGTCCCAAAATTA ATCACAAGTCGAAAAATCCTAAGTTTAGTGTTACTCTATTACACCTTTTTATTTGTAAGTGTCCTTTCACAAA AGTTTTAAATTTTGCTCTTGTGCATTTTATTTACCTTTTCTTTTGTTGTTTGTGTCTTTGGTGACCTGCCAAC CATTAGACTTCAAAAAACAGCCTATAGCCAAGCTGCAGGATAAATGAACAC

##Evidence: Cat hair from the victim's coat You extract DNA from the cat hair that you recovered from the victim's coat. From this analysis, you get: * A 6-loci Short-Tandem-Repeat Profile of the cat * Mitochondrial DNA If you find a cat you want to compare this DNA to, you can match or exclude the cat as origin for this evidence. [[Go back to the lab->Forensic Lab]] #### 6-loci STR profile <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/cat_str.png', width=150> #### mitochondrial DNA >`mitochondrial_DNA_Cat_hair` TAATTATGGCTGAATCATCCGATATTTACACGCCAACGGAGCTTCTATATTCTTTATCTGCCTGTACATA CATGTAGGACGGGGAATATACTACGGCTCCTACACCTTCTCAGAGACATGAAACATTGGAATCATACTAT TATTTACAGTCATAGCCACAGCTTTTATGGGATACGTCCTACCATGAGGCCAAATGTCCTTCTGAGGAGC AACCGTAATCACTAACCTCCTGTCAGCAATTCCATACATCGGGACTGAACTAGTAGAATGAATCTGAGGG GGCTTCTCAGTAGACAAAGCCACCCTAACACGATTCTTTGCTTTCCACTTCATTCTTCCATTCATTATCT CAGCCTTAGCAGCAGTACACCTCTTATTCCTTCATGAAACAGGATCTAACAACCCCTCAGGAATTACATC CGATTCAGACAAAATCCCATTCCACCCATACTATACAATCAAAGACATCCTAGGTCTTCTAGTACTAGTT TTAACACTCATACTACTCGTCCTATTTTCACCAGACCTGCTAGGAGACCCAGACAACTACATCCCAGCCA ACCCTTTAAATACCCCTCCCCATATTAAACCTGAATGATACTTCCTATTCGCATACGCAATTCTCCGATC CATCCCCAACAAACTAGGGGGAGTCCTAGCCCTAGTACTCTCCATCCTAGTACTAGCAATCATTCCAATC CTCCACACCTCCAAACAACGAGGAATAATGTTTCGACCACTAAGCCAATGTCTATTCTGACTCCTAGTAG CGGATCTCCTAACCCTAACATGAATCGGTGGCCAACCTGTAGAACATCCATTCATCACCATCGGCCAACT AGCCTCCATCCTATATTTCTCAACCCTCCTAATCCTAATACCCATCTCAGGCATTATTGAAAACCGCCTA CTCAAATGAAGAGTCTTTGTAGTATATAAAATACTTTGGTCTTGTAAACCAAAAAAGGAGAACATATGCC CTCCCTAAGACTTCAAGGAAGAAGCAACAGCCCCACTATCAGCACCCAAAGCTGAAATTCTTTCTTAAAC TATTCCTTGCCAATACCAGAAAGCAACCCCATAACTTTCATAATTCATATATTGCATATACCCATACTGT GCTTGCCCAGTATGTCCTTATTTCCCACAAAAAAACCAAGTAAAAACCCCCAAGTACCACAACCCAAAAC ACACAATGTAAAATCACTCTATTAACCACCAACTCACCCCAGTTGGTATTATACACCCATATACATAAGA CATACTATGTATATCGTGCATTAATTGCTAGTCCCCATGAATATTAAGCATGTANNNNNNTTTATATATA TTACATAAGACATACTATGTATATCGTRCATTAATTGCTAGTCCCCATGAATATTAAGCATGTACAGTAG TTTATATATATTACATAAGACATACTATGTATATCGTRCATTAATTGCTAGTCCCCATGAATATTAAGCA TGTACAGTAGTTTATATATATTACATAAGACATGATAGTGCTTAATCGTGCATTTACCTTANNNNNNNNN NNNNNTCCTATGGACCTCAACTATCCCAAAGAGCTTAATCACCTGGCCTCGAGAAACCAGCAATCCTTGC TCGAACGTGTACCTCTTCTCGCTCCGGGCCCATTTCAACGTGGGGGTTTCTATAACGGAACTATACCTGG CATCTGGTTCTTACTTCAGGGTCATAAAATCCTTGAATCCAATCCTTCAA

##Evidence: White biological material from victim's pocket (unless:$white_material_analyzed is true)[You extract DNA from the white biological material. Unfortunately, it is very degraded, so you only manage to get a short sequence (see bottom of the page). You could figure out what kind of DNA it is by comparing it against a database, for example with <a href='https://blast.ncbi.nlm.nih.gov/Blast.cgi' target='_blank'>BLAST</a>. Looking at the BLAST results, you believe that the white material belongs to the species: (write down the latin name ''with all small letters'' in this format: felis catus) (input-box:2bind $white_material_species,"=XX=",1) [[Check the species->White Material Species]]](if:$white_material_analyzed is true)[ "Elephant DNA... I still can't believe it!" Why would your victim have ivory in his pocket?] [[Go back to the lab->Forensic Lab]] ####DNA from white material >`DNA_white_material_victim_pocket` ATAATCAACCTTATAATCACGCTACTAACCAATACTATACTAACATCACTTATAGTTCTAATCGCATGTT GACTGCTCCAAACATACAATTACTCAGAGAAAACAAGTCCATACGAATGCGGCTTTGATCCAGTAGGCTC TGCTCGCTTACCATTCTCAATAAAATTCTTCTTAGTAGCTATCACATTTCTCCTATTTGACCTAGAAATT GCATTACTCCTACCTTTACCCTGAGCCATCCAAGCTAATAATACAAGTCTAACACTTTTGATATCATTTA TATTAATCATTCTCTTAGCTATTGGCTTAGCCTATGAATGACTCCATAAAGGCCTTGAATGAACCAAATA TG

##Evidence: Spores/Pollen from the victim's coat You consult the forensic botanist, who looks at the spores/pollen under a microscope. They tell you that it is definitely some sort of fungal spores. They further tell you that fungal spores can look very similar and that you should probably do a phylogenetic analysis to find out, which fungus the spores belong to. Lucky for you, the forensic botanist is a fungi enthusiast. They have walked the area around the village many times and drawn a map, which shows what types of fungi grow where. You extract DNA from the fungal spores and sequence it. You find out that the protein EF1alpha is often used to make phylogenetic trees of fungi. You locate the gene that codes for EF1alpha in your DNA and translate it so that you can put it in a tree with other fungi that are common in the area. You can find the protein sequence of EF1alpha from the spores on your victim below, as well as sequences of EF1alpha of the fungi that are common in the area. (set:$tree_instruction to true) [[Look at the fungi map->Fungi Map]] [[Instructions for making a phylogenetic tree->Instructions Tree]] [[Go back to the lab->Forensic Lab]] >`EF1alpha_Victim` MGKEKAHVNVVVIGHVDAGKSTTTGHLIYKCGGIDKRTIEKFEKEADELGKGSFKYAWVLDKLKAERERG ITIDIALWKFETPKYLVTVIDAPGHRDFIKNMITITSQADCAILVIAGGTGEFEAGISKDGQTREHALLS FTLGVRQLIVAVNKMDSTKWSEDRFNEIVKETSSFIKKVGYNPKTVAFVPISGWHGDNMIVETTNMPWYK GWSRETKAGVVKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGIIKAGMVVTFAP SNVTTEVKSVEMHHEQLAQGNPGDNVGFNVKNVSVKDIRRGNVASDSKNDPAKEAASFTAQVIVLNHPGQ IGAGYAPVLDCHTAHIACKFAELKEKIDRRTGKSLEDSPKFVKSGDAAIVKLVPSKPMCVESYNEYPPLG RFAVRDMRQTVAVGIIKSVEKTEKSGGKVTKSAEKANKKK >`EF1alpha_Amanita` MGKEKFHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERG ITIDIALWKFETPKFMVTVIDAPGHRDFIKNMITGTSQADCAILIIAAGTGEFEAGISKDGQTREHALLA FTLGVRQLIVAVNKMDTTKWSEDRFNEIVKETSTFIKKVGYNPKAVAFVPISGWHGDNMLEESPNMTWYK GWTKETKGGVVKGKTLLDAIDGIEPPVRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGLIKAGMVVTFAP SNVTTEVKSVEMHHEQLEAGMPGDNVGFNVKNVSVKDIRRGNVASDSKNDPAKEAASFNAQVIVLNHPGQ IGAGYAPVLDCHTAHIACKFAELLEKIDRRTGKSIEAAPKFVKSGDAAIVKLVPSKPMCVESYNEYPPLG RFAVRDMRQTVAVGIIKSVEKTDKSGGKVTKSAEKAAKKK >`EF1alpha_Coprinopsis` MGKEKAHVNVVVIGHVDAGKSTTTGHLIYKCGGIDKRTIEKFEKEADELGKGSFKYAWVLDKLKAERERG ITIDIALWKFETPKYLVTVIDAPGHRDFIKNMITITSQADCAILVIAGGTGEFEAGISKDGQTREHALLS FTLGVRQLIVAVNKMDSTKWSEDRFNEIVKETSSFIKKVGYNPKTVAFVPISGWHGDNMIVETTNMPWYK GWSRETKAGVVKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGIIKAGMVVTFAP SNVTTEVKSVEMHHEQLAQGNPGDNVGFNVKNVSVKDIRRGNVASDSKNDPAKEAASFTAQVIVLNHPGQ IGAGYAPVLDCHTAHIACKFAELKEKIDRRTGKSLEDSPKFVKSGDAAIVKLVPSKPMCVESYNEYPPLG RFAVRDMRQTVAVGIIKSVEKTEKSGGKVTKSAEKAAKKK >`EF1alpha_Phallus` QTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIVKETSTFIKKVGYNPKAVAFVPISGWHGDNMLE ESPNMTWYKGWTKELKSGTVKGKTLLDAIDAIEPPSRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGTIK AGMIVTFAPTNVTTEVKSVEMHHEQLEAGLPGDNVGFNVKNVSVKDIRRGNVCSDSKNDPAKEAASFNAQ VIVLNHPGQIGAGYAPVLDCHTAHIACKFAELLEKIDRRTGKAIEEAPKAIKSGDAAIVKMIPSKPMCVE TYNEYPPLGRFAVR >`EF1alpha_Parasola` AILIIAGGTGEFEAGISKDGQTREHALLAFTLGVRQLIVAINKMDTTKWSEDRFNEIVKETSNFVKKVGY NPKAVAFVPISGWHGDNMLEESVNMKWYKGWTRETKAGAVKGKTLLDAIDAIEPPVRPSDKPLRLPLQDV YKIGGIGTVPVGRVETGIIKAGMVVNFAPSNVTTEVKSVEMHHEQLEQGNPGDNVGFNVKNVSVKDIRRG NVASDSKNDPAKEAASFNAQVIVLNHPGQIGAGYAPVLDCHTAHIACKFAELKEKIDRRTGKSIEDAPKF VKSGDAAIVKLIPSKPM >`EF1alpha_Coprinellus` MGKEKAHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERG ITIDIALWKFETPKYMVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGTGEFEAGISKDGQTREHALLA FTLGVRQLIVAVNKMDTTKWSEDRFNEIVKETSNFIKKVGYNPKAVAFVPISGWHGDNMLEESPNMTWYK GWTREGKTGTLKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGIIKAGMVVTFAP TNVTTEVKSVEMHHEQLEQGNPGDNVGFNVKNVSVKDIRRGNVASDSKNDPAKEAASFNAQVIVLNHPGQ IGAGYAPVLDCHTAHIACKFAELIEKIDRRTGKSLEDAPKFVKSGDAAIVKLVPSKPMCVESYNEYPPLG RFAVRDMRQTVAVGIIKSVDKTDKSGGKVTKSAEKAAKKK

##Evidence: Mud on the victim's shoes You extract DNA from the mud on the victim's shoes and construct a microbiological soil profile using metabarcoding. If you find some sites that could be the crime scene, you can compare the microbiological soil profiles. This way, you can figure out which site most likely is the actual crime scene where Chris was killed. Without anything to compare it to, the soil profile is unfortunately not very useful... (if:(history: where its name contains "Fungi Map")'s length >= 1 and $soil_profiles_solved is not true)[You have a map of where which local fungi grow. If you figure out which fungus the spores on the victim belong to, then you can compare the mud to the soil at those sites.] [[Go back to the lab->Forensic Lab]] (if:$soil_profiles_solved is true)[ (set:$site5 to false)(set:$site11 to false)(set:$site19 to false)(set:$site22 to false)(set:$site23 to false) Which site is the actual crime scene? (checkbox: 2bind $site5,"5") (checkbox: 2bind $site11,"11") (checkbox: 2bind $site19,"19") (checkbox: 2bind $site22,"22") (checkbox: 2bind $site23,"23") [[Check the crime scene->Crime Scene]] If you need help figuring out how to compare the soil profiles of the potential crime scenes, you can go back to the lab and check the Methods page. [[Download the soil profiles again->Soil profiles]] ](unless:$soil_profiles_solved is true)[ (set: $site1 to false)(set: $site2 to false)(set: $site3 to false)(set: $site4 to false)(set: $site5 to false)(set: $site6 to false)(set: $site7 to false)(set: $site8 to false)(set: $site9 to false)(set: $site10 to false)(set: $site11 to false)(set: $site12 to false)(set: $site13 to false)(set: $site14 to false)(set: $site15 to false)(set: $site16 to false)(set: $site17 to false)(set: $site18 to false)(set: $site19 to false)(set: $site20 to false)(set: $site21 to false)(set: $site22 to false)(set: $site23 to false)(set: $site24 to false)(set: $site25 to false)(set: $site26 to false)(set: $site27 to false)(set: $site28 to false)(set: $site29 to false) (if:(history: where its name contains "Fungi Map")'s length >= 1)[ For which sites do you want to compare soil profiles? [[Go to the Fungi Map->Fungi Map]] (checkbox: 2bind $site1,"1") (checkbox: 2bind $site2,"2") (checkbox: 2bind $site3,"3") (checkbox: 2bind $site4,"4") (checkbox: 2bind $site5,"5") (checkbox: 2bind $site6,"6") (checkbox: 2bind $site7,"7") (checkbox: 2bind $site8,"8") (checkbox: 2bind $site9,"9") (checkbox: 2bind $site10,"10") (checkbox: 2bind $site11,"11") (checkbox: 2bind $site12,"12") (checkbox: 2bind $site13,"13") (checkbox: 2bind $site14,"14") (checkbox: 2bind $site15,"15") (checkbox: 2bind $site16,"16") (checkbox: 2bind $site17,"17") (checkbox: 2bind $site18,"18") (checkbox: 2bind $site19,"19") (checkbox: 2bind $site20,"20") (checkbox: 2bind $site21,"21") (checkbox: 2bind $site22,"22") (checkbox: 2bind $site23,"23") (checkbox: 2bind $site24,"24") (checkbox: 2bind $site25,"25") (checkbox: 2bind $site26,"26") (checkbox: 2bind $site27,"27") (checkbox: 2bind $site28,"28") (checkbox: 2bind $site29,"29") [[Give me the soil profiles->Soil profiles]]] ]

##Police Station At the police station, you can talk to different people. Once you have gathered evidence, the people will tell you different things. If you think you have solved the case, you can talk to your Captain. If you want to examine your evidence, go to the Forensic Lab. [[Go to the Forensic Lab->Forensic Lab]] Your witnesses/suspects: [[Talk to Ralph Benson, the victim's partner->Ralph Benson]] [[Talk to Theodore Howell, the victim's father->Theodore Howell]] [[Talk to Melissa Freeman, the victim's sister->Melissa Freeman]] [[Talk to Tommy Freeman, the victim's brother-in-law->Tommy Freeman]] [[Talk to Stephen Rodgers, the victim's boss->Stephen Rodgers]] [[Talk to Scott Rodgers, the victim's coworker and boss' son->Scott Rodgers]] When you know who the culprit is: [[Talk to the Captain->Captain]]

## Ralph Benson <img src="https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/ralph_benson.jpg" width=300> (if:visits is 0 or $saliva_ethnicity is false)[(align:"<==>")+(box:"XXXXXXX===")[Ralph wipes his nose as you walk in. His eyes are red and swollen. "Who would do this?!" His voice breaks as he asks the question. You put your hand on his shoulder. "I am so sorry for your loss." You wait for Ralph to collect himself and sit down. "I am so sorry that I have to ask you this. It is standard procedure." "You want my alibi?" You nod. "Well, I don't have one. I was at home, watching TV. Chris and I had had a fight, because I thought he was cheating. When he didn't come home, I figured he was with his new boyfriend..."]] (else-if:$saliva_ethnicity is true and $saliva_identified is false)[(align:"<==>")+(box:"XXXXXXX===")["You want my DNA?" Ralph doesn't seem surprised. In fact, his tone barely indicates that he is asking a question. "Yes. I'm sure you understand. We found some DNA on Chris and we found out that it was from a man of african descent." "It's fine. I figured you would want it sooner or later." You can now compare Ralph's STR profile to the saliva found on Chris. You can find his STR profile in the lab under "DNA Profiles" (set:$str_comparison to true)(set:$ralph_benson_str to true) [[Instructions for comparing STR profiles->Instructions STR profiles]]]](set:$ralph_str to true)(else-if:$saliva_ethnicity is true and $saliva_identified is true)[(align:"<==>")+(box:"XXXXXXX===")["Well, of course you found my DNA on him! We had had a fight, and he was leaving. I was trying to make up and so I kissed him before he left. You should stop talking to me and talk to that sister of his. Melissa was constantly accusing Chris of killing their mother for drug money. Drug money! He would never! He LOVED his mom! And if it wasn't her, it was her husband. Tommy doesn't have a backbone. They got married drunk in the spur of the moment and don't have a prenup. If Melissa divorces him, he loses a LOT of money. So, he just does everything she says."(set:$freeman_implicated to true)]] [[Go back to the Police station->Police Station]]

##Melissa Freeman <img src="https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/melissa_freeman.jpg" width=300> (if:$saliva_identified is false)[Melissa is sitting at the table with an empty expression. "I'm sorry for your loss", you say. She doesn't look up. "I'm sorry to have to ask you this, I assure you, it's standard proce-" "Do you have siblings, detective?" "I don't see how that matters." "Chris got into drugs when he was just a teen, did lots of horrible things. But he was my baby brother and I still loved him, you know?" "Chris had a drug problem?", you ask. "Not for a long time. He got into it in high school, even got kicked out. But when our mother was killed 6 years ago, he turned it around. Clean, from one day to the other." You wait to see whether she says anything else. When she doesn't, you continue. "I'm sorry to have to ask you this, It's completely standard procedure. Where were you last night?" "Home, with my husband. We watched de Mol on satellite TV."](if:$saliva_identified is true and $freeman_implicated is true)["You think *I* killed Chris? Who put you up to this? Ralph? Oh please, he's such a wuss. Just because I commented once or twice how it was weird that Chris took off for days after our mother's murder. Didn't even come to the funeral. That's odd, don't you think?" "I don't know your mother's case", you reply. "Still, it's odd that her son, who had been a junkie for 8 years just vanishes, doesn't come to the funeral, and then comes back totally clean. Probably a guilty conscience." "I'm sorry if I upset you. Would you be willing to give a DNA sample?" She splutters. "Sure, go right ahead! I have *nothing* to hide. (set:$melissa_freeman_str to true)"] [[Go back to the Police Station->Police Station]]

## Tommy Freeman <img src="https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/tommy_freeman.jpg" width=300> (if:$saliva_identified is false)["Mr. Freeman?" "Yes?" "I'm detective Bits. Sorry to meet you under these circumstances." You shake his sweaty hand. "I'm sorry, I don't have much time, so I have to cut right to the chase: where were you last night?" "Oh, uhm. Of course... My wife and I were watching TV. You see, she loves this obscure Dutch TV show. It's called... the mold or something? Yes. We were watching it like every week when it's on."](if:$saliva_identified is true and $freeman_implicated is true)["Oh, Ralph said that, huh..." Tommy shifts in his seat. "You see, my wife doesn't like him, but Ralph is actually not a bad guy." His voice turns to hardly more than a whisper. "Can you keep something between us?" You raise your eyebrows. "Sure." "I can kind of see, why Ralph would think that Melissa killed her brother. They weren't exactly on good terms. But I know her. She can be hostile, but she still loved him. If you ask me, you should look at their dad. Theo is a real mess. Has been since before his wife's death. Rumour has it, she was about to leave him. Plus, and *please* don't tell my wife I said this... He's a gambler. Racked up a lot of debt. Chris bailed him out a few times... until he didn't." You write down some notes. "Okay, sure. I'll look into that. In the meantime, would you consent to giving a DNA sample? "What, me? Uhm. I mean, I guess I have nothing to hide, so... okay." (set:$tommy_freeman_str to true)(set:$theo_implicated to true)] [[Go back to the Police Station->Police Station]]

## Theodore Howell <img src="https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/theodore_howell.jpg" width=300> (if:$theo_implicated is not true and $ralph_benson_str is not true)[You hear wailing from inside the interview room. You knock and the noises stop. You wait a few seconds before you walk in. "Mr. Howell, I am so sorry about your son." You hand Mr. Howell a tissue. "He was a good boy. He had some troubles, but he was a good kid. Good heart, you know? So much of his mom in him." "Your wife is not around anymore?" "No, she was murdered 6 years ago. Love of my life. The case is still open." "Look, I'm sorry I have to ask this, but... where were you last night?" "You think *I* killed my son?" "No, Sir, I have to ask everyone." "Well, I was home. Alone. I didn't go out at all yesterday."](if:$theo_implicated is not true and $ralph_benson_str is true)["Ralph? No way. That boy is an angel. After my wife died, he took care of Chris. It cannot possibly have been him."](if:$theo_implicated is true and $not_your_father is not true)["*Excuse me*?" You had already been dreadind this conversation. Mr. Howell is fuming. "When Mr. Freeman told us about the gambling, we checked your financials. It seems like he was right. You do spend a lot of money in casinos and on online poker." "So?" "Well, you are also getting a lot of money from an offshore account." "I don't see how that is any of your business, Detective." "It is if your son wanted to stop paying your gambling debts and that made you mad." "How dare you?!" Mr. Howell spits on the floor in you direction. "Here. My DNA. Go and check it. You better apologize once you realize that I'm innocent."(set:$theodore_howell_str to true)](if:$not_your_father is true and $white_material_analyzed is not true)[It looks like Theodore Howell doesn't yet have anything to say to you. If you analyze more of your evidence, that will change.](if:$not_your_father is true and $white_material_analyzed is true)["No, you're lying! You're lying!" "I'm sorry, Mr. Howell, but DNA doesn't lie." "So you're saying... My son wasn't my son at all?" He buries his face in his hands and starts sobbing. You watch him cry, trying to decide whether it would be more awkward to stay or to leave. You're about to give up when you hear Mr. Howell saying something under is breath that sounds like "that bastard". "Excuse me, could you repeat that?" Mr. Howell collects himself and clears his throat. "It was Stephen." "Who?" "Stephen Rodgers." "Why?" "His business is tangled up in all kinds of illegal activities. They almost got busted when my wife found out that they were smuggling ivory." "How did she find out?" "Stephen told me that she walked into his office in a bad moment, but *he swore to me* that there was nothing more to it. That they didn't have an affair. That bastard! He killed her." "Stephen Rodgers killed your wife?" "Yes. When she found out." "How long have you known?" "For a few years. He confessed to me, crying. He said he didn't mean to, he said he was sorry. Promised, he'd give Chris a job for the rest of his life. Paid off my gambling debt... a few times, actually." "But why would Stephen Rodgers kill your son?" Before Mr. Howell has a chance to say anything, you answer your own question. "Elephant DNA... Excuse me Mr. Howell" You leave the room. (set:$stephen_rodgers_implicated to true)] [[Go to the Police Station->Police Station]]

##Stephen Rodgers <img src="https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/stephen_rodgers.jpg" width=300> (if:$stephen_rodgers_implicated is not true)["Chris Howell, killed. A damn shame, that is." Stephen Rodgers lets out a deep sigh. "How well did you know the victim?" "Well, I've known him since he was born! Theo and I have been friends since we were kids, our sons basically grew up together. After Chris got clean, I gave him a job. He was damn good at it, too!" "So you don't think that Chris relapsed?" "No, no. He was clean. He was always on time for work, and he was always clear-headed. I actually wanted to promote him!" "Could you tell me where you were last night?" "In my office, working." "All night? Anyone who can vouch for that?" "Yes, all night. I have a pull-out couch in my office that I sometimes sleep on. And no, I was alone."](if:$stephen_rodgers_implicated is true and $stephen_is_the_father is not true)[Mr. Rodgers shakes his head. "Oh, Theo, Theo, Theo..." "So, you're saying he's lying?" "Maybe he's lying, or maybe he doesn't know what's real anymore. That poor guy has been through so much, first his wife, and now Chris." "Did you kill his wife and pay to keep him quiet?" "Of course not, that's ludicrous! Ivory smuggling?! Murder?! Come on, he sounds delusional." "Is Chris your biological son?" "Chris? What? No... It can't be!" His eyes go wide. "Was he... mine?" "Well, he wasn't Theodore Howell's." "C-can you... can you check?" "Sure, just give me a DNA sample."(set:$stephen_rodgers_str to true)](if:$stephen_is_the_father is true)["So... Chris was my son?" Stephen starts crying silently. "I wish I would have known..." "Mr. Rodgers, there is one more thing..." "Yes?" "Somebody who shares half your DNA is the one who killed Chris." Mr. Rogers' face darkens. "Scott...", he growls, "that stupid boy. What was he thinking?!" "He might have been trying to protect you." "Oh, please, as if I need protection! Stupid boy." "I don't know, Mr. Rogers. Chris was carrying around ivory when he died." "So what? There's no way that anyone can connect that to my company."] [[Go to the Police Station->Police Station]]

##Scott Rodgers <img src="https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/scott_rodgers.jpg" width=300> (unless:$stephen_is_the_father is true)["Hello Mr. Rodgers, I am Detective Bits." He smiles at you. "Call me Scott!" "Okay, Scott! I'm sorry we have to meet under these circumstances." "Yeah, it's really sad that Chris is dead." "How well did you know him?" "Phew... not well. I mean, we kind of grew up together, but when he started using, we kinda grew apart. I guess he works-... worked in our company the last few years, but we didn't really interact much." "Where were you last night?" "Last night? I was up late playing videogames." "Can anyone corroborate that?" He frowns. "No, I guess not. Why?" "Standard procedure. I will be back later!"](if:$stephen_is_the_father is true and $murder_solved is not true)[All the color drains from Scott's face. "W-why do you want my DNA?" "The killer shares half your father's DNA, just like Chris." "Do I have to give you a sample?" "Yes, considering the evidence we have, we can compel you to give us a sample." "I guess I don't have a choice then."(set:$scott_rodgers_str to true)](if:$murder_solved is true)[ "Yeah, I know... the DNA matches. Damn bottle... Chris had found out about the ivory smuggling that my dad does on the side. It's not like it's hurting anyone! Except the elephants, maybe... but they're just animals." "Chris called me, because he thought I didn't know. He even brought some with him in case I didn't believe him! He hid it somehwere before I arrived, that's why I couldn't leave him there. He said he wanted to give me a heads up, so that I could get out in time before law enforcement was going to take a closer look at the business. But I already knew about the ivory smuggling. And I didn't want my dad to go to prison... or for all the money to be lost. Why did Chris have to ruin everything?!" You have solved the murder. If the task list in the lab is empty, you can go to the Captain to complete the game. ] [[Go back to the Police Station->Police Station]]

##Fungi Map In the map below, you can see at which sites you can find which fungi. <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/fungi_map.png' width=800> [[Go back to the lab->Forensic Lab]] [[Go to the mud evidence->Victim Mud]]

## The Captain (if:$murder_solved is not true)["Oh hey, detective Bits! What a shame, that Howell murder. It looks like you are still in the process of collecting evidence, let me know once you have solved the case. If you have already solved the murder, but are still seeing this message, check your task list in the forensic lab to see whether there are still any open questions." What we know for now: (if:$crime_scene_found is not true)[* The victim wasn't killed where he was found](if:$crime_scene_found)[* The victim was killed at a site with a growth of Coprinopsis mushrooms and there was blood on the murder weapon](if:$blood_not_victims is true)[* The blood on the murder weapon was not the victim's and is therefore most likely the culprit's](if:$blood_not_victims is true and $blood_ethnicity is true)[* The blood evidence is from a man with European descent](if:$white_material_analyzed is true)[* The victim carried a white substance in his pocket that contained elephant DNA](if:$not_your_father is true and $double_check)[* Theodore Howell is not Chris' biological father](if:$yes_your_sister is true)[* Mitochondrial DNA shows that Chris Howell and Melissa Freeman did in fact have the same mother](if:$stephen_is_the_father is true)[* Stephen Rodgers is Chris Howell's biological father * Stephen Rodgers is not a match for the blood from the crime scene, but he shares half his alleles with the DNA from the crime scene.]](if:$murder_solved is true)[So, Scott Rodgers killed Chris Howell, because Chris found out that the Rodgers' business was smuggling ivory and was going to go public? That is wild! Let's see whether we can bust Stephen Rodgers for the smuggling... and the murder of Mrs. Howell. But that is for another day. Good job Detective, you have solved the case. Close the tab to end the game.]

(if:$soil_profiles_solved is true)[If you want to download the soil profiles again, you can do that <a href='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/soil_profiles.csv'>here</a>. [[Instructions for comparing soil profiles->Instruction Soil Profiles]] [[Go back to the lab->Forensic Lab]] ] (if:$site1 is false and $site2 is false and $site3 is false and $site4 is false and $site5 is true and $site6 is false and $site7 is false and $site8 is false and $site9 is false and $site10 is false and $site11 is true and $site12 is false and $site13 is false and $site14 is false and $site15 is false and $site16 is false and $site17 is false and $site18 is false and $site2 is false and $site2 is false and $site2 is false and $site19 is true and $site20 is false and $site21 is false and $site22 is true and $site23 is true and $site24 is false and $site25 is false and $site26 is false and $site27 is false and $site28 is false and $site29 is false)[Download the soil profile for the chosen sites from <a href='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/soil_profiles.csv'>here</a>. [[Instructions for comparing soil profiles->Instruction Soil Profiles]] [[Go back to the lab->Forensic Lab]] (set:$soil_profiles_solved to true) ] (unless:$site1 is false and $site2 is false and $site3 is false and $site4 is false and $site5 is true and $site6 is false and $site7 is false and $site8 is false and $site9 is false and $site10 is false and $site11 is true and $site12 is false and $site13 is false and $site14 is false and $site15 is false and $site16 is false and $site17 is false and $site18 is false and $site2 is false and $site2 is false and $site2 is false and $site19 is true and $site20 is false and $site21 is false and $site22 is true and $site23 is true and $site24 is false and $site25 is false and $site26 is false and $site27 is false and $site28 is false and $site29 is false)[(unless:$soil_profiles_solved is true)[Make sure to check at which sites the right fungus grows. The police department doesn't have enough money to waste on sequencing the wrong soil metagenome... It seems like you didn't choose the right combination of sites. Make sure to check the fungi map! (link-undo:"Go back")]]

##Instructions: Analyzing soil profiles You have gotten the microbial abundance profiles of the five potential crime scenes in .csv format. To determine which site was the crime scene, you have to compare the profiles and identify which site's microbiome clusters most closely with the mud on the victim's shoes. For this, you have to: * set your working directory correctly * load the abundance table, with making the first column the row names * normalize the abundance table * make a euclidian distance matrix for the soil profiles * cluster the soil profiles based on complete linkage * check the cladogram of the clustering for which site clusters together with the mud sample If you do not remember how to do that, check your R code (or the instructions) of the Werkcollege on 8th June about the Griftpark. You only need 5 or 6 lines of code, and each line corresponds to a list item above. [[Go back to Methods->Methods]] [[Go back to the Lab->Forensic Lab]]

##Methods (if:$soil_profiles_solved is true)[[[Instructions for examining the soil profiles ->Instruction Soil Profiles]]] (if:$str_comparison is true)[[[Instructions for comparing STR profiles->Instructions STR profiles]]] (if:$tree_instruction is true)[[[Instructions for making a phylogenetic tree->Instructions Tree]]] (if:$ethnicity_instructions is true)[[[Instructions for determining the ethnicity of a DNA sample->Instructions ethnicity]]] (if:$instructions_sry is true)[[[Instructions for comparing SRY genes or mitochondrial DNA->Instructions SRY mtDNA]]] [[Go back to the lab->Forensic Lab]]

##Crime scene (unless:$site5 is false and $site11 is false and $site19 is false and $site22 is false and $site23 is true)[ <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/crime_scene_false.jpg' width=612> You find some feathers, and some animal hair (probably dog or cat). Nothing is out of the ordinary. (link-undo:"Go back")](if:$site5 is false and $site11 is false and $site19 is false and $site22 is false and $site23 is true)[(set:$crime_scene_found to true)(set:$blood_not_victims to false) <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/crime_scene_true.jpg' width=612> On the ground, there is a smashed heavy glass bottle close to a giant pool of dried blood. Upon closer examination, there is some blood on some of the shards that belonged to the bottleneck. Maybe the blood is the culprit's? [[Go to the Lab->Forensic Lab]]]

## Evidence: Blood sample from the crime scene (unless:$blood_not_victims is true)[(set:$blood_yes_victims to false)First, you have to compare the STR profile of the crime scene to that of Chris Howell, the victim, himself. Is it the same DNA? <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/STR_crimescene_chris.png' height=600> (set:$str_comparison to true) (checkbox: 2bind $blood_yes_victims,"The blood is the victim's") (checkbox: 2bind $blood_not_victims,"The blood is not the victim's") [[Check->Check Blood Evidence]] [[Instructions for comparing STR profiles->Instructions STR profiles]] ](if:$blood_not_victims is true and $blood_ethnicity is not true)[Check the ethnicity of the blood sample using the SNP profile for ethnicity identification. [[Instructions for determining the ethnicity of the DNA sample->Instructions ethnicity]](set:$ethnicity_instructions to true) Which region is this sample from? (dropdown: bind $blood_region,"Choose region...", "africa","america","east asia","europe","oceania") [[Check->Check Blood Ethnicity]]] #### 8-loci STR profile <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/evidence_saliva.png', width=150> #### SNP profile for ethnicity identification AAAGCCGATTAATTAAAACCCTAGTTGAGAAAAACCTTTTGGTTCCAATAAACCAATTCCCCTTCCGG #### SRY gene >`SRY_gene_blood_evidence` TGACCTTCATTTTATGGAGAGAAACAAGCTATAACATGTAGTATCTAAGCTGATTAGAAGAACTAAAAAGAGA AGCTCATACTTGTGCATCAGAAGGTAAATGAAAGAGCGAAGTTACCTCTTTGTTTTAAGGAAGAAAGGAAAAT TGTGGATGTCATCTGTTTTCTGTTTACATATTTCAGGCATGGATAGCCACAATGTGATTTTAAGACGGTTAGT TACAACTGATTTGAAAAAAAAAAAAAATGCTTCACTCTATGAGAAATTTCTTCCCAAGTATGAAACCTTGTTT TTACAGGCAATTTCCTATACTTTGAAAAAATCAAAATAATAAAGTAAAAGAAAAATAATTCAGGTGAAGTTAG AGAAAAAAACAGGCAGCATTATTTTAAAGTTGTAAACTATTTTGTTTACTTATAGTTTAATTTAAATGTAGTA GATATGCATTTGTAAGGTTCTTCGGCTCAGGTAGGAGATCATTCTATTTCCCACTGCACCCTACTTCATCCTC CCACTGGCAAATAATTAGATTATCCCTGGGAAAAAAAGATGCCAGTAAAATTGATCATGTTTAAATGCATCAG TTGCTAGGTGATTTATCTGATTAAGTCTTGAAACAGTAGAACCTAGCAATTAAAGTGAGCATTAACTTCTACC TACCAAATCAGAAGACTATTCTAACTTTTTGAGAATTAGATGTTGAAAATATGGCCCATGAATTTAGCATGGT TAAAATAAAAAACATGCAAACAAAACAAACCCAGCATCTTGAAAGGCCATTTGACTCTAAAGTCCCAAAAATA ATCACAAGTCTAAAAATCCTAAGTTTAGTGTTACTCTATTACACCTTTTTATTTGTTAGTGTCCTTTCACAAA AGTTTTAAATTTTGCTCTTGTGCATTTTATTTACCTTTTCTTTTGTTGTTTGTGTCTTTGGTGACCTGCCAAC CATTAGACTTCAAAAAACAGACTATAGCCAAGCTGCAGGATAAATGAACAC

##Species of the white material (if:$white_material_species is 'loxodonta africana')[(set:$white_material_analyzed to true) "Wait what?" The forensic botanist must have heard your surprise, because they come over. "What's up, Bits?" "My victim had traces of... elephant DNA in his pocket" "Elephant? Could the test be wrong? Or contaminated?" You recheck the quality of the DNA and the e-value of your BLAST search. "Contaminated? How would I even be able to contaminate the sample with elephant DNA of all things?! No, no, it's definitely mitochondrial elephant DNA... extracted from a white material..." "Ivory?" You nod. "Couldn't really think of anything else." "But wait... Isn't that illegal?" "Very." But why would your victim have carried ivory around? [[Go back to the lab->Forensic Lab]]] (unless:$white_material_species is 'loxodonta africana')[You should run the test again. Something doesn't seem right. (link-undo:"Go back")]

##Available DNA-Profiles (if:$not_your_father is true and $double_check is not true)[Using the SRY genes below, figure out whether Chris is really not Theodore Howell's biological son. How many non-identities are there between Theodore and Chris Howell's SRY genes? (Just put in the number) (input-box:2bind $sry_differences,"=XX=",1) [[Check->Check SRY Theo Chris]] [[Instructions for comparing SRY genes->Instructions SRY mtDNA]]] (if:$double_check is true and $yes_your_sister is not true)[Using the mitochondrial DNA below, figure out whether Chris and Melissa are siblings in their maternal line. How many non-identities are there between Melissa Freeman's and Chris Howell's mitochondrial DNA? (Just put in the number) (input-box:2bind $mtDNA_differences,"=XX=",1) [[Check->Check mtDNA Melissa Chris]] [[Instructions for comparing mitochondrial DNA->Instructions SRY mtDNA]]] (if:$saliva_ethnicity is true and $ralph_benson_str is true )[* [[Compare the STR profiles of the saliva and Ralph Benson->Saliva vs Ralph]]](if:$blood_not_victims is true and $theodore_howell_str is true)[* [[Compare the STR profiles of the blood at the crime scene and Theodore Howell->Blood vs Theo]]](if:$blood_not_victims is true and $melissa_freeman_str is true)[* [[Compare the STR profiles of the blood at the crime scene and Melissa Freeman->Blood vs Melissa]]](if:$blood_not_victims is true and $tommy_freeman_str is true)[* [[Compare the STR profiles of the blood at the crime scene and Tommy Freeman->Blood vs Tommy]]](if:$blood_not_victims is true and $stephen_rodgers_str is true)[* [[Compare the STR profiles of Chris, the blood at the crime scene, and Stephen Rodgers->Blood vs Stephen]]](if:$blood_not_victims is true and $scott_rodgers_str is true)[* [[Compare the STR profiles of the blood at the crime scene, and Scott Rodgers->Blood vs Scott]]] [[Go back to the lab->Forensic Lab]] ###Chris Howell, the victim <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/chris_howell_str.png' width=150> >`sry_gene_chris_howell` TGACCTTCATTTTATGGAGAGAAACAAGCTATAACATGTAGTATCTAAGCTGATTAGAAGAACTAAAAAGAGA AGCTCATACTTGTGCATCAGAAGGTAAATGAAAGAGCGAAGTTACCTCTTTGTTTTAAGGAAGAAAGGAAAAT TGTGGATGTCATCTGTTTTCTGTTTACATATTTCAGGCATGGATAGCCACAATGTGATTTTAAGACGGTTAGT TACAACTGATTTGAAAAAAAAAAAAAATGCTTCACTCTATGAGAAATTTCTTCCCAAGTATGAAACCTTGTTT TTACAGGCAATTTCCTATACTTTGAAAAAATCAAAATAATAAAGTAAAAGAAAAATAATTCAGGTGAAGTTAG AGAAAAAAACAGGCAGCATTATTTTAAAGTTGTAAACTATTTTGTTTACTTATAGTTTAATTTAAATGTAGTA GATATGCATTTGTAAGGTTCTTCGGCTCAGGTAGGAGATCATTCTATTTCCCACTGCACCCTACTTCATCCTC CCACTGGCAAATAATTAGATTATCCCTGGGAAAAAAAGATGCCAGTAAAATTGATCATGTTTAAATGCATCAG TTGCTAGGTGATTTATCTGATTAAGTCTTGAAACAGTAGAACCTAGCAATTAAAGTGAGCATTAACTTCTACC TACCAAATCAGAAGACTATTCTAACTTTTTGAGAATTAGATGTTGAAAATATGGCCCATGAATTTAGCATGGT TAAAATAAAAAACATGCAAACAAAACAAACCCAGCATCTTGAAAGGCCATTTGACTCTAAAGTCCCAAAAATA ATCACAAGTCTAAAAATCCTAAGTTTAGTGTTACTCTATTACACCTTTTTATTTGTTAGTGTCCTTTCACAAA AGTTTTAAATTTTGCTCTTGTGCATTTTATTTACCTTTTCTTTTGTTGTTTGTGTCTTTGGTGACCTGCCAAC CATTAGACTTCAAAAAACAGACTATAGCCAAGCTGCAGGATAAATGAACAC >`mitochondria_CR_region_chris_howell` TCCAGTCTTGTAAACCGGAGATGAAAAGCTTTTTCCAAGGACAAATCAGAGAAAAAGTCTTTAACTCCACCAT TAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCAGC CAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCAACCATGAATGTTGTACG GTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACA AGCAAGTACAGCAATCAAGCCTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCTCACCCACTAGGA TACCAAAAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTC AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAA TATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATC CGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGA TGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGG TATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTGTGATTCCTGC CTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATT AATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAA ATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACA AAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCACTTTTAACAGTCACCCC CCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACGAATCTCATCAATACAACCCCCGCCCATCCTAC CCAGCACACACACACCGCTGCTAACCCCATACCCCTAACCAACCAAACCCCAAAGACACCCCCCACAGTTTAT GTAGCTTACCTCCTCAAAGC ###Suspects (if:$ralph_benson_str is true)[* Ralph Benson, the victim's partner <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/ralph_benson_str.png' width=150> >`sry_gene_ralph_benson` TGACCTTCATTTTATGGAGAGAAACAAGCTATAACATGTAGTATCTAAGCTGATTAGAAGAACTAAAAAGAGA AGCTCATACTTGTGCATCAGAAGGTAAATGAAAGAGTGAAGTTACCTCTTTGTTTTAAGGAAGAAAGGAAAAT TGTGGATGTCATCTGTTTTCTGTTTACATATTTCAGGCACGGATAGCCACAATGTGATTTTAAGACGGTTAGT TACAACTGATTTGAAAAAAAAAAAAAATGCTTCACTCTATGAGAAATTTCTTCCCAAGTATGAAACCTTGTTT TTACAGGCAATTTCCTATACTTTGAAAAAATCAAAATAATAAAGTAAAAGAAAAATAATTCAGGTGAAGTTAG AGAAAAAAACAGGCAGCATTATTTTAAAGTTGTAAACTATTTTGTTTACTTAAAGTTTAATTTACATGTAGTA GATATGCATTTGTAAGGTTCTTCGGCTCAGGTAGGAGAGCATTCTTTTTCCCACTGCACCCTACTTCATCCTC CCACTGGCAAATAATTAGATTATCCCTGGAAAAAAAAGATGCCAGTAAAATTGATCATGTTTAAATGCATCAG TTGCTAGGTGATTTATCTGATTAAGTCTTGAAACAGTAGAACCTAGCAATTAAAGTGAGCATTAACTTCTACC TACCAAATCAGAAGACTATTCTAACTTTTTGAGAATTAGATGTTGAAAATATGGCCCATGAATTTAGCTTGGT TAAAATAAAAAACATGCAAACAAAACAAACCCAACATCTTGAAAGGACATTTGACTCTAAAGTCCCAAAATTA ATCACAAGTCGAAAAATCCTAAGTTTAGTGTTACTCTATTACACCTTTTTATTTGTAAGTGTCCTTTCACAAA AGTTTTAAATTTTGCTCTTGTGCATTTTATTTACCTTTTCTTTTGTTGTTTGTGTCTTTGGTGACCTGCCAAC CATTAGACTTCAAAAAACAGCCTATAGCCAAGCTGCAGGATAAATGAACAC](if:$theodore_howell_str is true)[* Theodore Howell, the victim's father <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/theodore_howell_str.png' width=150> >`sry_gene_theodore_howell` TGACCTTCATTTTATGGAGAGAAACAAGCTATAACATGTAGTATCTAAGCTGATTAGAAGACCTAAAAAGAGA AGCTCATACTTGTGCATCAGAAGGTAAATGAAAGAGTGAAGTTACCTCTTTGTTTTAAGGAAGAAAGGAAAAT TGTGGATGTCATCTGTTTTCTGTTTAGATATTTCAGGCATGGATAGCCACAATGTGATTTTAAGACGGTTAGT TACAACTGATTTGAAAAAAAAAAAAAATGCTTCACTCTATGACAAATTTCTTCCCAAGTATGAAACCTTGTTT TTACAGGCAATTTCCTATACTTTGAAAAAATCAAAATAATAAAGTAAAAGAAAAATAATTCAGGTGAAGTTAG AGAAAAAAACAGGCAGCATTATTTTAAAGTTGAAAACTATTTTGTTTACTTACAGTTTAATTTACATGTAGTA GATATGCATTTGTAAGGTTCTTCGGCTCAGGTAGGAGATCATTTTATTTCCCACTGCACCCTACTTCATCCTC CCACTGGCAAATAATTAGATTATCCCTGGGAAAAAAAGATGCCAGTAAAATTGATCATGTTTAAATGCATCAG TTGCTAGGTGATTTATCTGATTAAGTCTTGAAACAGTAGAACCTAGCAATTAAAGTGAGCATTAACTTCTACC TACCAAATCAGAAGACTATTCTAACTTTTTGAGAATTAGATGTTGAAAATATGGCCCATGAATTTAGCATGGT TAAAATAAAAAACATGCAAACAAAACAAACCCAACATCTTGAAAGGACATTTGACTCTAAAGTCCCAAAAATA ATCACAAGTGTAAAAATCCTAAGTTTAGTGTTACTCTATTACACCTTTCTATTTGTAAGTGTCTTTTCACAAA AGTTTTAAATTTTGCTCTTGTGCATTTTATTTACCTTTCCTTTTGTTGTTTGTGTCTTTGGTGACCTGCCAAC CATTAGACTTCAAAAAACAGCCTATAGCCAAGCTGCAGGATAAATGAACAC](if:$melissa_freeman_str is true)[* Melissa Freeman, the victim's sister <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/melissa_freeman_str.png' width=150> >`mitochondria_CR_region_melissa_freeman` TCCAGTCTTGTAAACCGGAGATGAAAAGCTTTTTCCAAGGACAAATCAGAGAAAAAGTCTTTAACTCCACCAT TAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCAGC CAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCAACCATGAATGTTGTACG GTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACA AGCAAGTACAGCAATCAAGCCTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCTCACCCACTAGGA TACCAAAAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTC AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAA TATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATC CGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGA TGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGG TATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTGTGATTCCTGC CTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATT AATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAA ATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACA AAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCACTTTTAACAGTCACCCC CCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACGAATCTCATCAATACAACCCCCGCCCATCCTAC CCAGCACACACACACCGCTGCTAACCCCATACCCCTAACCAACCAAACCCCAAAGACACCCCCCACAGTTTAT GTAGCTTACCTCCTCAAAGC] (if:$tommy_freeman_str is true)[* Tommy Freeman, the victim's brother-in-law <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/tommy_freeman_str.png' width=150> >`sry_gene_tommy_freeman` TGACCTTCAGCTTATGGAGAGAAACAAGCTATAACATGTAGTATCTAAGCTGATTAGAAGAACTAAAAAGAGA AGCTCATACTTGTGCATCAGAAGGTAAATGAAAGAGTGAAGTTACCTCTTTGTTTTAAGAAAGAAAGGAAAAT TGTGGATGTCATCTGTTTTCTGTTTACATATTTCAGGAATGGATAGCCACAATGTGATTTTAAGACGGTTAGT TACAACTGATTTGAAAAAAAAAAAAAATGCTTCACTCTATGAGAAATTTCTTCCCAAGTATGAAACCTTGTTT TTACAGGCAATTTCCTATACTTTGAAAAAATCAAAATAATAAAGTAAAAGAAAAATAATTCAGGTGAAGTTAG AGAAAAAAACAGGCAGCATTATTTTAAAGTTGTAAACTATTTTGTTTACTTATAGTTTAATTTACATGTAGTA GATATGCATATGTAAGGTTCTTCGGCTCAGGTAGGAGATCATTCTATTTCCCACTGCACACTACTTCATCCTC CCACTGGCAAATAATTAGATTATCCCTGGGAAAAAAAGATGCCAGTAAAATTGATCATGTTTAAATGCATCAG TTGCTAGGTGATTTATCTGATTAAGTCTTGAAACAGTAGATCCTAGCAATTAAAGTGAGCATTAACTTCTACC TACCAAATCAGAAGACTATTCTAACTTTTTGAGAATTAGATGTTGAAAATATGGCCCATGAATTTAGCATGGT TAAAATAAAAAACATGCAAACAAAACAAACCCAACATCTTGAAAGGACATTTGACTCTAAAGTCCCAAAAATA ATCACAAGTCTAAAAATCCTAAGTTTAGTGTTACTCTATTACACCTTTTTATTTGTAAGTGTCCTTTCACAAA AGTTTTAAATTTTGCTCTTGTGCATTTTATTTACCTTTTCTTTTGTTGTTTGTGTCTTTGGTGACCTGCCAAC CATTAGACTTCAAAAAACAGCCTATAGCCAAGCTGCAGGATAAATGAACAC](if:$stephen_rodgers_str is true)[* Stephen Rodgers, the victim's boss <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/stephen_rodgers_str.png' width=150> >`sry_gene_stephen_rodgers` TGACCTTCATTTTATGGAGAGAAACAAGCTATAACATGTAGTATCTAAGCTGATTAGAAGAACTAAAAAGAGA AGCTCATACTTGTGCATCAGAAGGTAAATGAAAGAGCGAAGTTACCTCTTTGTTTTAAGGAAGAAAGGAAAAT TGTGGATGTCATCTGTTTTCTGTTTACATATTTCAGGCATGGATAGCCACAATGTGATTTTAAGACGGTTAGT TACAACTGATTTGAAAAAAAAAAAAAATGCTTCACTCTATGAGAAATTTCTTCCCAAGTATGAAACCTTGTTT TTACAGGCAATTTCCTATACTTTGAAAAAATCAAAATAATAAAGTAAAAGAAAAATAATTCAGGTGAAGTTAG AGAAAAAAACAGGCAGCATTATTTTAAAGTTGTAAACTATTTTGTTTACTTATAGTTTAATTTAAATGTAGTA GATATGCATTTGTAAGGTTCTTCGGCTCAGGTAGGAGATCATTCTATTTCCCACTGCACCCTACTTCATCCTC CCACTGGCAAATAATTAGATTATCCCTGGGAAAAAAAGATGCCAGTAAAATTGATCATGTTTAAATGCATCAG TTGCTAGGTGATTTATCTGATTAAGTCTTGAAACAGTAGAACCTAGCAATTAAAGTGAGCATTAACTTCTACC TACCAAATCAGAAGACTATTCTAACTTTTTGAGAATTAGATGTTGAAAATATGGCCCATGAATTTAGCATGGT TAAAATAAAAAACATGCAAACAAAACAAACCCAGCATCTTGAAAGGCCATTTGACTCTAAAGTCCCAAAAATA ATCACAAGTCTAAAAATCCTAAGTTTAGTGTTACTCTATTACACCTTTTTATTTGTTAGTGTCCTTTCACAAA AGTTTTAAATTTTGCTCTTGTGCATTTTATTTACCTTTTCTTTTGTTGTTTGTGTCTTTGGTGACCTGCCAAC CATTAGACTTCAAAAAACAGACTATAGCCAAGCTGCAGGATAAATGAACAC](if:$scott_rodgers_str is true)[* Scott Rodgers, the victim's coworker and boss' son <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/scott_rodgers_str.png' width=150> >`sry_gene_scott_rodgers` TGACCTTCATTTTATGGAGAGAAACAAGCTATAACATGTAGTATCTAAGCTGATTAGAAGAACTAAAAAGAGA AGCTCATACTTGTGCATCAGAAGGTAAATGAAAGAGCGAAGTTACCTCTTTGTTTTAAGGAAGAAAGGAAAAT TGTGGATGTCATCTGTTTTCTGTTTACATATTTCAGGCATGGATAGCCACAATGTGATTTTAAGACGGTTAGT TACAACTGATTTGAAAAAAAAAAAAAATGCTTCACTCTATGAGAAATTTCTTCCCAAGTATGAAACCTTGTTT TTACAGGCAATTTCCTATACTTTGAAAAAATCAAAATAATAAAGTAAAAGAAAAATAATTCAGGTGAAGTTAG AGAAAAAAACAGGCAGCATTATTTTAAAGTTGTAAACTATTTTGTTTACTTATAGTTTAATTTAAATGTAGTA GATATGCATTTGTAAGGTTCTTCGGCTCAGGTAGGAGATCATTCTATTTCCCACTGCACCCTACTTCATCCTC CCACTGGCAAATAATTAGATTATCCCTGGGAAAAAAAGATGCCAGTAAAATTGATCATGTTTAAATGCATCAG TTGCTAGGTGATTTATCTGATTAAGTCTTGAAACAGTAGAACCTAGCAATTAAAGTGAGCATTAACTTCTACC TACCAAATCAGAAGACTATTCTAACTTTTTGAGAATTAGATGTTGAAAATATGGCCCATGAATTTAGCATGGT TAAAATAAAAAACATGCAAACAAAACAAACCCAGCATCTTGAAAGGCCATTTGACTCTAAAGTCCCAAAAATA ATCACAAGTCTAAAAATCCTAAGTTTAGTGTTACTCTATTACACCTTTTTATTTGTTAGTGTCCTTTCACAAA AGTTTTAAATTTTGCTCTTGTGCATTTTATTTACCTTTTCTTTTGTTGTTTGTGTCTTTGGTGACCTGCCAAC CATTAGACTTCAAAAAACAGACTATAGCCAAGCTGCAGGATAAATGAACAC]

##Comparing STR profiles There are different ways of comparing DNA profiles. Usually, 13-17 loci in a person's DNA are amplified. These loci are known to contain microsatellite regions with short-tandem-repeats. Then, either a gel electropheresis is done, or a capillary electrophoresis. Analyzing microsatellite regions purely bioinformatically is still difficult, as the short-tandem-repeats make it difficult to assemble the region from NGS reads. For this case, we will be using 8 loci (=16 alleles) to compare DNA profiles. We will be using the gel electrophoresis version, despite it being slightly outdated, because they are easier to read. Let's look at an example of three individuals: <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/instructions_STR.png', width=150> To compare two DNA profiles, you have to put them exactly next to each other. The first step is rather easy: Are any of the DNA profiles the same? Cleary not. If two STR profiles are from the same person, they have to **match exactly in all alleles**. There will be overlaps in some of the alleles between people, either because * The individuals are related * An allele on one of the loci happens to coincidentally have the same length in two individual * The resolution of the gel electrophoresis is not high enough to separate by a 2-3 nucleotide difference and the length looks the same. The second step: are any of these individuals related? Every person shares half their alleles with the person that gave the egg, and the other half with the person who gave the sperm. Now, if you look at the three individuals on top, you will see that for each allele of P1, either P2 or P3 have an allele that matches exactly. Therefore, P2 and P3 are P1's biological parents. This is important! **If an indivual doesn't share half the alleles with the other individual, they are not a biological parent/child!**. On the other hand, if individuals share significantly more than half of their alleles (>~55%), then the individuals are not just related, but there is evidence for incest within the family tree. ''Hint:'' If a line is suspiciously thick, then it could be that it is actually two lines right next to each other. So, if you only count 15 lines, but one of them is very thick, then it is probably two. [[Go back to the methods->Methods]] [[Go back to the lab->Forensic Lab]]

##Instructions: Tree making Additionally to the spores from the body, you have gotten five different sequences from fungi that are common in the area. To determine which type of fungus the spores belong to, you should make a phylogenetic tree with all the sequences and your sample and then check which fungus your sample groups with. To make the phylogenetic tree, go to <a href='https://www.ebi.ac.uk/Tools/msa/clustalo/' target='_blank'>https://www.ebi.ac.uk/Tools/msa/clustalo/</a>. Copy the six sequences in fasta format into the input text box. Alternatively, you can also save the sequences in a text file and then upload that under "Choose file". Click on "Submit" at the bottom. Making this tree will not take long. Once the job has finished, you can click on "Phylogenetic Tree" to see the tree that clustal omega has made from your sequences. You can choose between 'Cladogram' and 'Real'. The fungus that the spores from the victim's coat group with is the fungus that probably grows around the crime scene. [[Go back to Methods->Methods]] [[Go back to the Lab->Forensic Lab]]

##Instructions: Ethnicity typing of a DNA sample When you have a human DNA sample in evidence, you also get a string of SNPs. It is 68 nucleotides long, and represents 2 alleles of 34 loci. To determine the ethnicity of your sample, you can use a tool called snipper at <a href='http://mathgene.usc.es/snipper/popchoosing5groups.html' target='_blank'>http://mathgene.usc.es/snipper/popchoosing5groups.html</a>. Under ''Step 1'', choose the marker set "34-plex (revised) with rs3827760". We want to use this set, as it is the most up-to-date. Make sure you read carefully, otherwise you will get an error! Under ''Step 2'', choose "5 populations". We don't know, which ethnicity a sample belongs to, so we want to have the most diverse set. Unter ''Step 3'', choose "Naive Bayes (Hardy-Weinberg principle applies)" At the bottom, there is an input box. Paste the SNP string into that box and click classify. The results will be displayed in a report. The easiest way to find out, how your sample compares to others, is to scroll down a bit and click on the button that says "View PCA plots" or "View 3D PCA plot". Check, with which ethnicity your sample groups together. [[Go back to Methods->Methods]] [[Go back to the lab->Forensic Lab]]

##Evidence: Saliva - Ethnicity (unless:$saliva_region is 'africa')[Are you sure? From the PCA, it doesn't really look like the sample is from someone with ancestors from $saliva_region... (link-undo:"Go back")](if:$saliva_region is 'africa' and $ralph_benson_str is not true)[The DNA is from someone of african descent? If one of your suspects is of african descent, you can compare their DNA to the DNA profile of the saliva. (set:$saliva_ethnicity to true) [[Go to the Lab->Forensic Lab]]]

##Checking the blood evidence (unless:$blood_yes_victims is false and $blood_not_victims is true)[Are you sure? Maybe check again](if:$blood_yes_victims is false and $blood_not_victims is true)[So, the blood evidence from the bottleneck is clearly not Chris'. This is good news! That means that the culprit likely cut themselves when they smashed the bottle over the victim's head. When you find out who the blood belongs to, you'll have your culprit! [[Go back to the lab->Forensic Lab]]]

##Evidence: Blood - Ethnicity (unless:$blood_region is 'europe')[Are you sure? From the PCA, it doesn't really look like the sample is from someone with ancestors from $blood_region... (link-undo:"Go back")](if:$blood_region is 'europe')[The DNA is from someone of european descent? If you have a suspect of european descent, you can compare the DNA to figure out if they match. (set:$blood_ethnicity to true) [[Go to the Lab->Forensic Lab]]]

##Compare Saliva DNA with Ralph Benson <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/STR_saliva_ralph.png' height=600> How many alleles do the saliva DNA profile and Ralph's DNA share? (dropdown: bind $saliva_ralph_shared_alleles, "0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16") [[Check->Check Saliva vs Ralph]]

##Compare Crime Scene DNA with Theodore Howell <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/STR_crimescene_theo_chris.png' height=600> How many alleles do the blood DNA profile and Theodore's DNA share? (dropdown: bind $blood_theo_shared_alleles, "0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16") How many alleles do Theodore's and Chris' DNA share? (dropdown: bind $chris_theo_shared_alleles, "0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16") [[Check->Check Blood vs Theo]]

##Compare Crime Scene DNA with Melissa Freeman <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/STR_crimescene_melissa.png' height=600> How many alleles do the blood DNA profile and Melissa's DNA share? (dropdown: bind $blood_melissa_shared_alleles, "0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16") [[Check->Check Blood vs Melissa]]

##Compare Crime Scene DNA with Tommy Freeman <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/STR_crimescene_tommy.png' height=600> How many alleles do the blood DNA profile and Tommy's DNA share? (dropdown: bind $blood_tommy_shared_alleles, "0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16") [[Check->Check Blood vs Tommy]]

##Compare Crime Scene DNA with Stephen Rodgers <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/STR_crimescene_stephen.png' height=600> How many alleles do the blood DNA profile and Stephen's DNA share? (dropdown: bind $blood_stephen_shared_alleles, "0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16") <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/STR_chris_stephen.png' height=600> How many alleles do Chris' and Stephen's DNA share? (dropdown: bind $chris_stephen_shared_alleles, "0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16") [[Check->Check Blood vs Stephen]]

##Compare Crime Scene DNA with Scott Rodgers <img src='https://tbb.bio.uu.nl/tina/genomica/forensic_binf/images/STR_crimescene_scott.png' height=600> How many alleles do the blood DNA profile and Scott Rodger's DNA share? (dropdown: bind $blood_scott_shared_alleles, "0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16") [[Check->Check Blood vs Scott]]

##Compare Saliva DNA with Ralph Benson (unless:$saliva_ralph_shared_alleles is '16')[Are you sure? Maybe check again...](if:$saliva_ralph_shared_alleles is '16')[That's right! The DNA profile is a perfect match! The saliva from the victim's cheek belongs to Ralph Benson. (set:$saliva_identified to true) [[Go back to the STR profiles->STR Profiles]] [[Go back to the lab->Forensic Lab]]]

##Compare Blood DNA with Theo ####Blood vs. Theo (unless:$blood_theo_shared_alleles is '0' or $blood_theo_shared_alleles is '1' or $blood_theo_shared_alleles is '2')[Are you sure? Maybe check again...](if:$blood_theo_shared_alleles is '0' or $blood_theo_shared_alleles is '1' or $blood_theo_shared_alleles is '2')[Since they share $blood_theo_shared_alleles allele(s), the profiles are clearly not a match. Looks like Theodore is not your killer...] (unless:$chris_theo_shared_alleles is '0' or $chris_theo_shared_alleles is '1' or $chris_theo_shared_alleles is '2')[Are you sure? Maybe check again...] #### Chris vs. Theo (if:$chris_theo_shared_alleles is '0' or $chris_theo_shared_alleles is '1' or $chris_theo_shared_alleles is '2')[Huh... Chris and Theo share $chris_theo_shared_alleles allele(s)? Looks like you have uncovered quite the family secret! Just to be sure, maybe you should double-check by comparing Chris' and Theo's SRY-genes.(set:$not_your_father to true)(set:$yes_your_sister to false)(set:$double_check to false)(set:$instructions_sry to true) [[Instructions for comparing SRY-genes and mitochondrial genes->Instructions SRY mtDNA]] [[Go back to the STR profiles->STR Profiles]] [[Go back to the lab->Forensic Lab]]]

##Comparing SRY genes and mitochondrial DNA ####SRY gene The SRY gene can be used to identify relatives in the y-chromosome-carrying line. Father and son, as well as y-carrying siblings, sometimes even cousins, should have identical (100%!) SRY-genes. If the SRY-genes are not identical, then the two samples likely don't belong to first-degree y-carrying relatives. ####Mitochondrial DNA Unlike the SRY gene, mitochondrial DNA is given through the egg. The mother will give the mitochondrial DNA to all offspring. For our example, the mitochondrial DNA also has to be 100% identical for to individuals to be first-degree relatives in the maternal line. ####Comparing genes You can go to <a href='https://blast.ncbi.nlm.nih.gov/Blast.cgi'>the BLAST website</a>. There, scroll down past the BLAST flavours and click on "Global Align". Instead of having just one text box to put in a sequence like in regular BLAST, here you can put in one sequence on top, and one on the bottom, and compare them to each other. On the results page, go to the alignment tab, where you can see the number of identities. Remember: for this example, anything below 100% identity means that it is not a match. [[Go back to Methods->Methods]] [[Go back to the Lab->Forensic Lab]]

##Compare Blood DNA with Melissa (unless:$blood_melissa_shared_alleles is '0' or $blood_melissa_shared_alleles is '1' or $blood_melissa_shared_alleles is '2')[Are you sure? Maybe check again...](if:$blood_melissa_shared_alleles is '0' or $blood_melissa_shared_alleles is '1' or $blood_melissa_shared_alleles is '2')[Since they share $blood_melissa_shared_alleles allele(s), the profiles are clearly not a match. Looks like Melissa is not your killer... Then again, the fact that you extracted an SRY gene from the blood at the crime scene could have already told you that. [[Go back to the STR profiles->STR Profiles]] [[Go back to the lab->Forensic Lab]]]

##Compare Blood DNA with Tommy (unless:$blood_tommy_shared_alleles is '0' or $blood_tommy_shared_alleles is '1' or $blood_tommy_shared_alleles is '2')[Are you sure? Maybe check again...](if:$blood_tommy_shared_alleles is '0' or $blood_tommy_shared_alleles is '1' or $blood_tommy_shared_alleles is '2')[Since they share $blood_tommy_shared_alleles allele(s), the profiles are clearly not a match. Looks like Tommy is not your killer... [[Go back to the STR profiles->STR Profiles]] [[Go back to the lab->Forensic Lab]]]

##Check Blood vs Stephen (unless:$blood_stephen_shared_alleles is '8' and $chris_stephen_shared_alleles is '8')[Are you sure? Maybe check again...](if:$blood_stephen_shared_alleles is '8' and $chris_stephen_shared_alleles is '8')[So, Stephen shares 8 alleles with the blood from the crime scene? That means that he is not the killer. However, that means that the killer shares half his DNA. If one of your suspects shares half of Stephen's DNA, this information should be enough to get a DNA sample.(set:$stephen_is_the_father to true) Stephen also shares 8 alleles with Chris! That means, that he definitively is Chris' biological father. [[Go back to the STR profiles->STR Profiles]] [[Go back to the lab->Forensic Lab]]]

## Compare SRY genes of Theodore Howell and Chris Howell (unless:$sry_differences is '16')[Are you sure? $sry_differences? Maybe check again.](if:$sry_differences is '16')[There are indeed 16 differences between Theodore and Chris Howell's SRY genes. Looks like they aren't biologically related. (set:$double_check to true) [[Go back to the DNA profiles->STR Profiles]] [[Go back to the Lab->Forensic Lab]]]

## Compare mitochondrial DNA of Melissa and Chris (unless:$mtDNA_differences is '0')[Are you sure? Maybe check again.](if:$mtDNA_differences is '0')[Melissa's and Chris' mitochondrial DNA is identical! So, they are siblings through their mother. That is good to know. (set:$yes_your_sister to true) [[Go back to the DNA profiles->STR Profiles]] [[Go back to the Lab->Forensic Lab]]]

##Compare Crime Scene DNA with Scott Rodgers (unless:$blood_scott_shared_alleles is '16')[Are you sure? Maybe check again...](if:$blood_scott_shared_alleles is '16')[That's right! The DNA profile is a perfect match! The blood from the crime scene belongs to Scott Rodgers. If you want to know his motive, you should probably talk to him again. (set:$murder_solved to true) [[Go back to the STR profiles->STR Profiles]] [[Go back to the lab->Forensic Lab]]]