visit to john hopkins
DESCRIPTION
Visit to John Hopkins. Aravinda Chakravarti and other researchers. People and labs. Aravinda Chakravarti - human geneticist specializing in complex traits. Dan Arking much work with SNP arrays Andy McCallion - Gene regulation, especially enhancers in zebrafish. - PowerPoint PPT PresentationTRANSCRIPT
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Visit to John Hopkins
Visit to John Hopkins
Aravinda Chakravarti and other researchersAravinda Chakravarti
and other researchers
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People and labsPeople and labs• Aravinda Chakravarti - human geneticist specializing in complex traits.– Dan Arking much work with SNP arrays
• Andy McCallion - Gene regulation, especially enhancers in zebrafish.
• Akhilesh Pandey - runs human protein reference database.
• Ada Hamosh - runs curation side of OMIM.– Joanna Amberger - curator
• David Valle - psychiatric genetics• David Cutler - SNP haplotyping, phasing.
• Aravinda Chakravarti - human geneticist specializing in complex traits.– Dan Arking much work with SNP arrays
• Andy McCallion - Gene regulation, especially enhancers in zebrafish.
• Akhilesh Pandey - runs human protein reference database.
• Ada Hamosh - runs curation side of OMIM.– Joanna Amberger - curator
• David Valle - psychiatric genetics• David Cutler - SNP haplotyping, phasing.
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Some of Arivinda’s ProjectsSome of Arivinda’s Projects• Likes projects that use a variety of techniques. Likes developing methods.
• Hirschprung’s disease.• Cardiac sudden death & QT interval.
• Hypertension• Autism
• Likes projects that use a variety of techniques. Likes developing methods.
• Hirschprung’s disease.• Cardiac sudden death & QT interval.
• Hypertension• Autism
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Hirschprung’s DiseaseHirschprung’s Disease• Lower parts of the gut, or in severe cases all of the gut lacks innervation.
• Patients used to due from blocked gut during infancy. Surgery now helps.
• 4x more common in males.• 1/5000 infants affected.• ~10% of siblings of affected are also affected.
• Lower parts of the gut, or in severe cases all of the gut lacks innervation.
• Patients used to due from blocked gut during infancy. Surgery now helps.
• 4x more common in males.• 1/5000 infants affected.• ~10% of siblings of affected are also affected.
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Genetics of Hirschprung’sGenetics of Hirschprung’s• Mutations in 6 genes significantly increase risk for Hirschprungs.– RET,PHOX2B,NRTN, L1CAM, GDNF, EDN3
• These genes identified since 90’s via linkage.
• Aravinda’s lab sequenced RET in many patients.– They estimate that coding mutations in RET cause 3% of cases. Mutations here tend to be fairly penetrant.
– A common SNP (~25% minor allele frequency) in a conserved noncoding region, increases Hirschprung’s risk by 4x, especially in males.
• Mutations in 6 genes significantly increase risk for Hirschprungs.– RET,PHOX2B,NRTN, L1CAM, GDNF, EDN3
• These genes identified since 90’s via linkage.
• Aravinda’s lab sequenced RET in many patients.– They estimate that coding mutations in RET cause 3% of cases. Mutations here tend to be fairly penetrant.
– A common SNP (~25% minor allele frequency) in a conserved noncoding region, increases Hirschprung’s risk by 4x, especially in males.
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Sudden Cardiac Death & QT Sudden Cardiac Death & QT
• Seemingly healthy individuals die suddenly from heart failure (VTach/V Fib).– ~2/3rds have some coronary artery disease but not enough to explain death
– ~1/3rd are from people with no detectable heart disease.
• Associated with long or very short QT interval (which can be observed in an EKG).
• Hard to get samples from sudden death victims, since they are dead.
• Initial study focused on QT interval as a quantitative trait. – Lots of data and DNA samples from Framingham Heart Study and others are available.
• Seemingly healthy individuals die suddenly from heart failure (VTach/V Fib).– ~2/3rds have some coronary artery disease but not enough to explain death
– ~1/3rd are from people with no detectable heart disease.
• Associated with long or very short QT interval (which can be observed in an EKG).
• Hard to get samples from sudden death victims, since they are dead.
• Initial study focused on QT interval as a quantitative trait. – Lots of data and DNA samples from Framingham Heart Study and others are available.
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Genetic Analysis of QT IntervalsGenetic Analysis of QT Intervals• Nature Genetics article by Dan Arking et al.• Treated QT interval as a continuous trait.• Large association study using Affy 100k chip.• Took extreme 200 subjects showing most extreme QT’s out of 4000 total subjects.
• Validated results on 4400 independent subjects.
• Used simple ANOVA stats to calculate association at each SNP.
• NOS1AP (CAPON) varients explain 1.5% of QT interval variation.– 3 SNPs in conserved noncoding regions, one of which likely explains this variation.
• Nature Genetics article by Dan Arking et al.• Treated QT interval as a continuous trait.• Large association study using Affy 100k chip.• Took extreme 200 subjects showing most extreme QT’s out of 4000 total subjects.
• Validated results on 4400 independent subjects.
• Used simple ANOVA stats to calculate association at each SNP.
• NOS1AP (CAPON) varients explain 1.5% of QT interval variation.– 3 SNPs in conserved noncoding regions, one of which likely explains this variation.
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Genetic analysis of Sudden DeathGenetic analysis of Sudden Death• Small samples of sudden death victims from ambulances are available.
• Currently lab is doing an association study based on the Affy 500k chip.
• At end of data gathering stage, just starting data analysis.– Evaluating algorithms, Abacus vs. BRLM– There is an annoying amount of variation between lots of Affy chips.
• Small samples of sudden death victims from ambulances are available.
• Currently lab is doing an association study based on the Affy 500k chip.
• At end of data gathering stage, just starting data analysis.– Evaluating algorithms, Abacus vs. BRLM– There is an annoying amount of variation between lots of Affy chips.
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HypertensionHypertension• Also a quantitative trait.• Aravinda’s involved with many analysis– Meta-analysis of many linkage studies– Explaining differential effects of salt on hypertension in various populations to evolutionary history (salt/heat tolerant populations more susceptable to salt-sensitive hypertension).
– Candidate gene approaches– Also has turned up regulatory mutants.
• Also a quantitative trait.• Aravinda’s involved with many analysis– Meta-analysis of many linkage studies– Explaining differential effects of salt on hypertension in various populations to evolutionary history (salt/heat tolerant populations more susceptable to salt-sensitive hypertension).
– Candidate gene approaches– Also has turned up regulatory mutants.
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Aravinda’s Lab & AutismAravinda’s Lab & Autism
• Focusing on autistics with language difficulties.
• Using affy 500k chip • Have family information• Use chip data first in linkage study, then use same data with transmission-disequilibrium-test for association study within candidate regions.
• Have found some relatively common varients that contribute to risk.
• Colleagues at UCLA have found rarer, higher risk variants.
• Focusing on autistics with language difficulties.
• Using affy 500k chip • Have family information• Use chip data first in linkage study, then use same data with transmission-disequilibrium-test for association study within candidate regions.
• Have found some relatively common varients that contribute to risk.
• Colleagues at UCLA have found rarer, higher risk variants.
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Aravinda’s Thinking about Association vs. Linkage
Aravinda’s Thinking about Association vs. Linkage• Ultimately need to take kinship into account in both association and linkage studies.
• For every region in the genome, given a population, can make a binary tree based on genetic similarity in that region.
• In a sense are looking for regions where cases show up on one side of tree and controls on another.
• There will be some such regions by chance common kinship *within*that*region.
• The causative mutations should be in such a region as well.
• A promising technique is to estimate the relatedness overall within the population, and use that to scale significance of associations.
• Ultimately need to take kinship into account in both association and linkage studies.
• For every region in the genome, given a population, can make a binary tree based on genetic similarity in that region.
• In a sense are looking for regions where cases show up on one side of tree and controls on another.
• There will be some such regions by chance common kinship *within*that*region.
• The causative mutations should be in such a region as well.
• A promising technique is to estimate the relatedness overall within the population, and use that to scale significance of associations.
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Andy McClellanAndy McClellan
• Postdoc’d in Aravinda’s lab.• Has done functional assays of RET mutants in mouse and zebrafish.
• Interested in transcriptional regulation in general, especially enhancers/suppressors.
• Finding many mammalian enhancers work in zebrafish, even in absense of overt sequence conservation.
• Doing zebrafish versions of many things Eddy Rubin & Len Pinnocio doing in mouse.– Higher throughput in zebrafish, and can observe embryo over time.
• Postdoc’d in Aravinda’s lab.• Has done functional assays of RET mutants in mouse and zebrafish.
• Interested in transcriptional regulation in general, especially enhancers/suppressors.
• Finding many mammalian enhancers work in zebrafish, even in absense of overt sequence conservation.
• Doing zebrafish versions of many things Eddy Rubin & Len Pinnocio doing in mouse.– Higher throughput in zebrafish, and can observe embryo over time.
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A technique Andy is examining:A technique Andy is examining:
• Hypothesis - enhancers/repressors are brought into physical proximity with promoters they regulate.
• Method:– Cross-link cells with formaldehyde– Digest DNA with restriction enzyme– Ligate with ligase– Sequences near each other in nucleus will form little circles.
– Do PCR with primers from one sequence. Sequence PCR results and see what else is there.
• Hypothesis - enhancers/repressors are brought into physical proximity with promoters they regulate.
• Method:– Cross-link cells with formaldehyde– Digest DNA with restriction enzyme– Ligate with ligase– Sequences near each other in nucleus will form little circles.
– Do PCR with primers from one sequence. Sequence PCR results and see what else is there. primer
primer
enhancer fragment
promoter fragment
restriction &ligation site
restriction &ligation site
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Akhilesh PandeyAkhilesh Pandey• Human Protein Reference Database.– http://www.hprd.org/– Large scale effort curating human proteins and protein-protein interactions out of the literature.
– Curation team was 70 at it’s peak, all PhDs in India.
– Web works is also quite nice.– Contains much more pathway stuff than reactome.
– Web works are also quite nice.
• Human Protein Reference Database.– http://www.hprd.org/– Large scale effort curating human proteins and protein-protein interactions out of the literature.
– Curation team was 70 at it’s peak, all PhDs in India.
– Web works is also quite nice.– Contains much more pathway stuff than reactome.
– Web works are also quite nice.
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Ada Hamosh & OMIMAda Hamosh & OMIM
• Pediatrician and geneticist• Took over running OMIM from Victor McKusick.
• Software and web developmentfor OMIM is at NCBI.
• Curation is mostly at John Hopkins with some additional contractors. McKusick still does some of the curation. Only ~7 curators.
• Pediatrician and geneticist• Took over running OMIM from Victor McKusick.
• Software and web developmentfor OMIM is at NCBI.
• Curation is mostly at John Hopkins with some additional contractors. McKusick still does some of the curation. Only ~7 curators.
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OMIM continuedOMIM continued• OMIM is 100% literature based.• Genetic varients in OMIM:
– All varients in first paper describing gene/disease link.
– Beyond this try to have most important and common disease-causing variants.
– No shortcut to mapping variants to genome, all taken from literature directly, which is a hodge-podge.
• Curators are skeptical of controlled vocabularies– Prefer medical thesaurus
• http://www.nlm.nih.gov/research/umls/about_umls.html#Metathesaurus
– Human disease phenotypes are especially a moving target because doctors intervene! Therapies generally improve over time.
• OMIM is 100% literature based.• Genetic varients in OMIM:
– All varients in first paper describing gene/disease link.
– Beyond this try to have most important and common disease-causing variants.
– No shortcut to mapping variants to genome, all taken from literature directly, which is a hodge-podge.
• Curators are skeptical of controlled vocabularies– Prefer medical thesaurus
• http://www.nlm.nih.gov/research/umls/about_umls.html#Metathesaurus
– Human disease phenotypes are especially a moving target because doctors intervene! Therapies generally improve over time.
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David ValleDavid Valle• Pediatrician, works with OMIM
• Discussed primarily psychiatric genetics.
• Pediatrician, works with OMIM
• Discussed primarily psychiatric genetics.
David CutlerDavid Cutler• Implements software for working with Affymetrix chips, from gridding to calling.
• His Abacus algorithm has been adopted by Affy now.
• Also works on haplotype phasing.
• Implements software for working with Affymetrix chips, from gridding to calling.
• His Abacus algorithm has been adopted by Affy now.
• Also works on haplotype phasing.
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Suggestions for hgGenomeSuggestions for hgGenome
• Overall fewer than at King lab (reflecting hgGenome design for association studies….)
• Support Merlin output, which gives chromosome/centimorgans as position in a number of different maps.
• Support Affy ID’s as well as dbSNP.• Consider adding some optional smoothing.
• Overall fewer than at King lab (reflecting hgGenome design for association studies….)
• Support Merlin output, which gives chromosome/centimorgans as position in a number of different maps.
• Support Affy ID’s as well as dbSNP.• Consider adding some optional smoothing.
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Suggestion for track showing phased SNPs and copy number.
Suggestion for track showing phased SNPs and copy number.
s001
s002
s003
s004
s005
s006
s007
s008
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Other suggestionsOther suggestions• Ways to make it easier to find candidate genes within linkage/association peaks.
• Making it more obvious that something has actually happened when you make a custom track in table browser.
• Make it so that you can see OMIM ID from graphics page.
• Make links into Human Protein Reference Database.
• Ways to make it easier to find candidate genes within linkage/association peaks.
• Making it more obvious that something has actually happened when you make a custom track in table browser.
• Make it so that you can see OMIM ID from graphics page.
• Make links into Human Protein Reference Database.
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