Large-scale identity-by-descent mapping discovers rare haplotypes of large effect. Suyash Shringarpure 23andMe, Inc. ASHG 2017
|
|
- Isabella Moody
- 5 years ago
- Views:
Transcription
1 Large-scale identity-by-descent mapping discovers rare haplotypes of large effect Suyash Shringarpure 23andMe, Inc. ASHG
2 Why care about rare variants of large effect? Months from randomization 2
3 The 23andMe cohort is well-powered for rare variant associations 2M+ customers ~85% 700M+ consent to research survey questions answered 3
4 Rare variants of large effect are likely to be recent 4 (Lupski et al., 2011, Cell)
5 Recent variants identical-by-descent haplotypes A B C D E A B C D E IBD pairs (A.B), (B,C), (A,C), (E,) 5
6 IBD clusters as rare variant proxies IBD cluster : Group of samples with all / most pairs IBD with each other in a genomic region IBD clusters represent shared haplotypes, and therefore shared rare variants IBD mapping : inding IBD clusters enriched for cases 6
7 Outline IBD mapping method Experiments Next steps and conclusions 7
8 Step 1 : Infer IBD segments genomewide with IBD64 10 Mb 25 Mb A B C IBD64 D A,B B,C A,C E, E 8 (Henn et al., 2012, PLoS One)
9 Step 2 : Construct and cluster IBD graphs in windows A,B B,C A,C E, B A B A E C D A A D B D A E C D E C E C B E C B D MCL : Markov clustering ( org/mcl/man/m cl.html) 9
10 Step 3 : Choose candidate clusters to test B A E C D 2 cases, 4 controls PC1 = Binomial test (2 cases in a cluster of 3) PC2 = Binomial test (0 case in a cluster of 2) A B C D E PC3 = Binomial test (0 cases in a cluster of 1) 10
11 Step 4 : Logistic test with clusters and covariates Phenotype Cluster member? Age Sex M M 2 cases, 4 controls Logistic M 11
12 IBD mapping experiments Phenotype Population Sample size Number of IBD segments (millions) Breast or ovarian cancer European 114, Parkinson s disease Ashkenazi 43,173 1,
13 A rare haplotype of large effect in BRCA2 Phenotype: Breast or ovarian cancer Chromosome 13 Cluster = 31 cases, 29 controls Rest = cases, controls Cluster frequency = 0.05 % Odds ratio = P-value = 1.3e-12 13
14 A rare haplotype of large effect in LRRK2 Phenotype : Parkinson s disease Chromosome 12 Cluster = 125 cases, 547 controls Rest = 987 cases, controls Cluster frequency = 1.5 % Odds ratio = 9.42 P-value = 3.5e-68 14
15 Associated clusters tag rare protein-coding variants Phenotype Population Sample size Cluster size SNP (Gene) Population alt allele frequency (%) Cluster alt allele frequency (%) Breast or ovarian cancer European 114, rs / Ser1982Argfs (BRCA2) Parkinson s disease Ashkenazi 43, rs / G2019S (LRRK2)
16 Novel IBD mapping hit in JAG1 for prostate cancer Chromosome 20 Cluster = 14 cases, 40 controls Rest = cases, controls Cluster frequency = 0.049% Odds ratio = 8.22 P-value = 1.5e-7 16
17 JAG1 cluster overlaps a wide genomic region 17
18 JAG1 is associated with prostate cancer in literature 18
19 Next steps Test all clusters Generate phased IBD at scale Validate more hits by sequencing 19
20 Conclusions IBD mapping can tag rare variation that can be hard to impute and may only be accessible through sequencing. We show results of IBD mapping on the 23andMe cohort. IBD clusters can prioritize samples for sequencing. More improvements to be made in IBD inference and downstream association. 20
21 Acknowledgements 23andMe research participants David Hinds Vladimir Vacic Steve Pitts Robert Gentleman Adam Auton 23andMe Research Team 21
Combining genetic and exposure data significantly improves risk prediction for skin cancer
Combining genetic and exposure data significantly improves risk prediction for skin cancer Pierre Fontanillas, Babak Alipanahi, Michaela Johnson, Catherine Wilson, 23andMe Research Team, Steve Pitts, Robert
More informationCS2220 Introduction to Computational Biology
CS2220 Introduction to Computational Biology WEEK 8: GENOME-WIDE ASSOCIATION STUDIES (GWAS) 1 Dr. Mengling FENG Institute for Infocomm Research Massachusetts Institute of Technology mfeng@mit.edu PLANS
More informationIntroduction to Genetics and Genomics
2016 Introduction to enetics and enomics 3. ssociation Studies ggibson.gt@gmail.com http://www.cig.gatech.edu Outline eneral overview of association studies Sample results hree steps to WS: primary scan,
More informationGENOME-WIDE ASSOCIATION STUDIES
GENOME-WIDE ASSOCIATION STUDIES SUCCESSES AND PITFALLS IBT 2012 Human Genetics & Molecular Medicine Zané Lombard IDENTIFYING DISEASE GENES??? Nature, 15 Feb 2001 Science, 16 Feb 2001 IDENTIFYING DISEASE
More informationSUPPLEMENTARY FIGURES
SUPPLEMENTARY FIGURES Supplementary Figure 1 Regional association plots for genome-wide significant PCOS signals. Dots represents individual SNP association P-values (on the log10 scale) in the 23andMe
More informationAssociation mapping (qualitative) Association scan, quantitative. Office hours Wednesday 3-4pm 304A Stanley Hall. Association scan, qualitative
Association mapping (qualitative) Office hours Wednesday 3-4pm 304A Stanley Hall Fig. 11.26 Association scan, qualitative Association scan, quantitative osteoarthritis controls χ 2 test C s G s 141 47
More informationCompound heterozygosity Yurii S. Aulchenko yurii [dot] aulchenko [at] gmail [dot] com. Thursday, April 11, 13
Compound heterozygosity Yurii S. Aulchenko yurii [dot] aulchenko [at] gmail [dot] com 1 Outline Recessive model Examples of Compound Heterozygosity Compound Double Heterozygosity (CDH) test 2 Recessive
More informationBig Data Training for Translational Omics Research. Session 1, Day 3, Liu. Case Study #2. PLOS Genetics DOI: /journal.pgen.
Session 1, Day 3, Liu Case Study #2 PLOS Genetics DOI:10.1371/journal.pgen.1005910 Enantiomer Mirror image Methadone Methadone Kreek, 1973, 1976 Methadone Maintenance Therapy Long-term use of Methadone
More informationSupplementary Figure 1: Attenuation of association signals after conditioning for the lead SNP. a) attenuation of association signal at the 9p22.
Supplementary Figure 1: Attenuation of association signals after conditioning for the lead SNP. a) attenuation of association signal at the 9p22.32 PCOS locus after conditioning for the lead SNP rs10993397;
More informationDOES THE BRCAX GENE EXIST? FUTURE OUTLOOK
CHAPTER 6 DOES THE BRCAX GENE EXIST? FUTURE OUTLOOK Genetic research aimed at the identification of new breast cancer susceptibility genes is at an interesting crossroad. On the one hand, the existence
More informationGlobal variation in copy number in the human genome
Global variation in copy number in the human genome Redon et. al. Nature 444:444-454 (2006) 12.03.2007 Tarmo Puurand Study 270 individuals (HapMap collection) Affymetrix 500K Whole Genome TilePath (WGTP)
More informationNew Enhancements: GWAS Workflows with SVS
New Enhancements: GWAS Workflows with SVS August 9 th, 2017 Gabe Rudy VP Product & Engineering 20 most promising Biotech Technology Providers Top 10 Analytics Solution Providers Hype Cycle for Life sciences
More informationRare Variant Burden Tests. Biostatistics 666
Rare Variant Burden Tests Biostatistics 666 Last Lecture Analysis of Short Read Sequence Data Low pass sequencing approaches Modeling haplotype sharing between individuals allows accurate variant calls
More informationWhite Paper Estimating Complex Phenotype Prevalence Using Predictive Models
White Paper 23-12 Estimating Complex Phenotype Prevalence Using Predictive Models Authors: Nicholas A. Furlotte Aaron Kleinman Robin Smith David Hinds Created: September 25 th, 2015 September 25th, 2015
More informationOn Missing Data and Genotyping Errors in Association Studies
On Missing Data and Genotyping Errors in Association Studies Department of Biostatistics Johns Hopkins Bloomberg School of Public Health May 16, 2008 Specific Aims of our R01 1 Develop and evaluate new
More informationSupplementary Figure S1A
Supplementary Figure S1A-G. LocusZoom regional association plots for the seven new cross-cancer loci that were > 1 Mb from known index SNPs. Genes up to 500 kb on either side of each new index SNP are
More informationRelationship between genomic features and distributions of RS1 and RS3 rearrangements in breast cancer genomes.
Supplementary Figure 1 Relationship between genomic features and distributions of RS1 and RS3 rearrangements in breast cancer genomes. (a,b) Values of coefficients associated with genomic features, separately
More informationThe genetics of complex traits Amazing progress (much by ppl in this room)
The genetics of complex traits Amazing progress (much by ppl in this room) Nick Martin Queensland Institute of Medical Research Brisbane Boulder workshop March 11, 2016 Genetic Epidemiology: Stages of
More informationThe Foundations of Personalized Medicine
The Foundations of Personalized Medicine Jeremy M. Berg Pittsburgh Foundation Professor and Director, Institute for Personalized Medicine University of Pittsburgh Personalized Medicine Physicians have
More informationWhole-genome detection of disease-associated deletions or excess homozygosity in a case control study of rheumatoid arthritis
HMG Advance Access published December 21, 2012 Human Molecular Genetics, 2012 1 13 doi:10.1093/hmg/dds512 Whole-genome detection of disease-associated deletions or excess homozygosity in a case control
More informationSupplementary Figure 1. Principal components analysis of European ancestry in the African American, Native Hawaiian and Latino populations.
Supplementary Figure. Principal components analysis of European ancestry in the African American, Native Hawaiian and Latino populations. a Eigenvector 2.5..5.5. African Americans European Americans e
More informationComponents of heritability in an Icelandic cohort
Components of heritability in an Icelandic cohort Noah Zaitlen Harvard School of Public Health Conflict of Interest Disclosure Four of the authors (Helgason, Gudbjartsson, Kong, Stefansson) are shareholders
More information3) It is not clear to me why the authors exclude blond hair from the red hair GWAS, and blond and red hair from the brown hair GWAS.
Reviewer #1 (Remarks to the Author): The manuscript from Morgan et al. presents a fascinating in-depth look at the genetics of hair color in the UK Biobank collection. The authors examine nearly 350,000
More informationOutline. Identifying your risk for hereditary breast or ovarian cancer. Genetics 101. What causes cancer? Genetics
Identifying your risk for hereditary breast or ovarian cancer David Andorsky, MD Breanna Roscow, MS, CGC 303-993-0161 Outline Genetics and biology of hereditary cancer syndromes BRCA1 and BRCA2 Genetic
More informationQuality Control Analysis of Add Health GWAS Data
2018 Add Health Documentation Report prepared by Heather M. Highland Quality Control Analysis of Add Health GWAS Data Christy L. Avery Qing Duan Yun Li Kathleen Mullan Harris CAROLINA POPULATION CENTER
More informationWhite Paper Guidelines on Vetting Genetic Associations
White Paper 23-03 Guidelines on Vetting Genetic Associations Authors: Andro Hsu Brian Naughton Shirley Wu Created: November 14, 2007 Revised: February 14, 2008 Revised: June 10, 2010 (see end of document
More informationAdditional Disclosure
Additional Disclosure The Genetics of Prostate Cancer: Clinical Implications William J. Catalona, MD Collaborator with decode genetics, Inc. Non-paid consultant with no financial interest or support Northwestern
More informationThe Risk of Anti-selection in Protection Business from Advances in Statistical Genetics
The Risk of Anti-selection in Protection Business from Advances in Statistical Genetics Richard Russell, PhD Lead Health Data Scientist Stephen Courquin Head of UK Actuarial Research Peter Banthorpe SVP,
More informationChallenges in design and analysis of large register-based epidemiological studies
FMS/DSBS autumn meeting 2014 Challenges in design and analysis of large register-based epidemiological studies Caroline Weibull & Anna Johansson Department of Medical Epidemiology and Biostatistics (MEB)
More informationPaola Nicoletti, Harshad Devarbhavi, Ashish Goel, CE Eapen, Radha Venkatesan, Jane I Grove, Ann K Daly and Guruprasad P. Aithal
Genome-wide association study (GWAS) to identify genetic risk factors that increase susceptibility to antituberculosis drug-induced liver injury (ATDILI) Paola Nicoletti, Harshad Devarbhavi, Ashish Goel,
More informationNovember 9, Johns Hopkins School of Medicine, Baltimore, MD,
Fast detection of de-novo copy number variants from case-parent SNP arrays identifies a deletion on chromosome 7p14.1 associated with non-syndromic isolated cleft lip/palate Samuel G. Younkin 1, Robert
More informationSupplementary Figure 1. Quantile-quantile (Q-Q) plots. (Panel A) Q-Q plot graphical
Supplementary Figure 1. Quantile-quantile (Q-Q) plots. (Panel A) Q-Q plot graphical representation using all SNPs (n= 13,515,798) including the region on chromosome 1 including SORT1 which was previously
More informationNature Genetics: doi: /ng Supplementary Figure 1. SEER data for male and female cancer incidence from
Supplementary Figure 1 SEER data for male and female cancer incidence from 1975 2013. (a,b) Incidence rates of oral cavity and pharynx cancer (a) and leukemia (b) are plotted, grouped by males (blue),
More informationPirna Sequence Variants Associated With Prostate Cancer In African Americans And Caucasians
Yale University EliScholar A Digital Platform for Scholarly Publishing at Yale Public Health Theses School of Public Health January 2015 Pirna Sequence Variants Associated With Prostate Cancer In African
More informationAnalysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers
Analysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers Gordon Blackshields Senior Bioinformatician Source BioScience 1 To Cancer Genetics Studies
More informationStatistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies
Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies Stanford Biostatistics Workshop Pierre Neuvial with Henrik Bengtsson and Terry Speed Department of Statistics, UC Berkeley
More informationGWAS of HCC Proposed Statistical Approach Mendelian Randomization and Mediation Analysis. Chris Amos Manal Hassan Lewis Roberts Donghui Li
GWAS of HCC Proposed Statistical Approach Mendelian Randomization and Mediation Analysis Chris Amos Manal Hassan Lewis Roberts Donghui Li Overall Design of GWAS Study Aim 1 (DISCOVERY PHASE): To genotype
More informationDan Koller, Ph.D. Medical and Molecular Genetics
Design of Genetic Studies Dan Koller, Ph.D. Research Assistant Professor Medical and Molecular Genetics Genetics and Medicine Over the past decade, advances from genetics have permeated medicine Identification
More informationLinkage analysis: Prostate Cancer
Linkage analysis: Prostate Cancer Prostate Cancer It is the most frequent cancer (after nonmelanoma skin cancer) In 2005, more than 232.000 new cases were diagnosed in USA and more than 30.000 will die
More informationDetecting Identity by Descent and Homozygosity Mapping in Whole-Exome Sequencing Data
Detecting Identity by Descent and Homozygosity Mapping in Whole-Exome Sequencing Data Zhong Zhuang 1 *., Alexander Gusev 1., Judy Cho 3, Itsik e er 1,2 1 Department of Computer Science, Columbia University,
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTRY INFORMTION Supplementary Figure 1. Q-Q plot of RE/NIMH autism family TDT results. The quantile-quantile plot of the expected and observed P-values is shown. The blue circles represent the
More informationGENETIC TESTING FOR HEREDITARY BREAST AND OVARIAN CANCER BRCA1 BRCA2
GENETIC TESTING FOR HEREDITARY BREAST AND OVARIAN CANCER BRCA1 BRCA2 Coverage for services, procedures, medical devices and drugs are dependent upon benefit eligibility as outlined in the member's specific
More informationSupplementary Figure 1. Quantile-quantile (Q-Q) plot of the log 10 p-value association results from logistic regression models for prostate cancer
Supplementary Figure 1. Quantile-quantile (Q-Q) plot of the log 10 p-value association results from logistic regression models for prostate cancer risk in stage 1 (red) and after removing any SNPs within
More informationColorspace & Matching
Colorspace & Matching Outline Color space and 2-base-encoding Quality Values and filtering Mapping algorithm and considerations Estimate accuracy Coverage 2 2008 Applied Biosystems Color Space Properties
More informationHost Genomics of HIV-1
4 th International Workshop on HIV & Aging Host Genomics of HIV-1 Paul McLaren École Polytechnique Fédérale de Lausanne - EPFL Lausanne, Switzerland paul.mclaren@epfl.ch Complex trait genetics Phenotypic
More informationReviewers' comments: Reviewer #1 (Remarks to the Author):
Reviewers' comments: Reviewer #1 (Remarks to the Author): Major claims of the paper A well-designed and well-executed large-scale GWAS is presented for male patternbaldness, identifying 71 associated loci,
More informationDuring the hyperinsulinemic-euglycemic clamp [1], a priming dose of human insulin (Novolin,
ESM Methods Hyperinsulinemic-euglycemic clamp procedure During the hyperinsulinemic-euglycemic clamp [1], a priming dose of human insulin (Novolin, Clayton, NC) was followed by a constant rate (60 mu m
More informationDoing more with genetics: Gene-environment interactions
2016 Alzheimer Disease Centers Clinical Core Leaders Meeting Doing more with genetics: Gene-environment interactions Haydeh Payami, PhD On behalf of NeuroGenetics Research Consortium (NGRC) From: Joseph
More informationA rare variant in MYH6 confers high risk of sick sinus syndrome. Hilma Hólm ESC Congress 2011 Paris, France
A rare variant in MYH6 confers high risk of sick sinus syndrome Hilma Hólm ESC Congress 2011 Paris, France Disclosures I am an employee of decode genetics, Reykjavik, Iceland. Sick sinus syndrome SSS is
More informationGenetic Approaches to Alcoholism, Alcohol Abuse Susceptibility, and Therapeutic Response. Ray White Verona March
Genetic Approaches to Alcoholism, Alcohol Abuse Susceptibility, and Therapeutic Response Ray White Verona March 18. 2008 Craig Venter Genome 2,810,000,000 bases, 7.5-fold coverage 3,213,401 SNPs 85% in
More informationVariation in PNPLA3 is associated with outcomes. in alcoholic liver disease
Variation in PNPLA3 is associated with outcomes in alcoholic liver disease Chao Tian 1, Renee P. Stokowski 1, David Kershenobich 2, Dennis G. Ballinger 1,3, David A. Hinds 1 1. Perlegen, 2021 Stierlin
More informationIntroduction to linkage and family based designs to study the genetic epidemiology of complex traits. Harold Snieder
Introduction to linkage and family based designs to study the genetic epidemiology of complex traits Harold Snieder Overview of presentation Designs: population vs. family based Mendelian vs. complex diseases/traits
More informationComputer Science, Biology, and Biomedical Informatics (CoSBBI) Outline. Molecular Biology of Cancer AND. Goals/Expectations. David Boone 7/1/2015
Goals/Expectations Computer Science, Biology, and Biomedical (CoSBBI) We want to excite you about the world of computer science, biology, and biomedical informatics. Experience what it is like to be a
More informationFigure S2. Distribution of acgh probes on all ten chromosomes of the RIL M0022
96 APPENDIX B. Supporting Information for chapter 4 "changes in genome content generated via segregation of non-allelic homologs" Figure S1. Potential de novo CNV probes and sizes of apparently de novo
More informationExample HLA-B and abacavir. Roujeau 2014
Example HLA-B and abacavir Roujeau 2014 FDA requires testing for abacavir Treatment with abacavir is generally well tolerated, but 5% of the patients experience hypersensitivity reactions that can be life
More informationConditions. Name : dummy Age/sex : xx Y /x. Lab No : xxxxxxxxx. Rep Centre : xxxxxxxxxxx Ref by : Dr. xxxxxxxxxx
Name : dummy Age/sex : xx Y /x Lab No : xxxxxxxxx Rep Centre : xxxxxxxxxxx Ref by : Dr. xxxxxxxxxx Rec. Date : xx/xx/xx Rep Date : xx/xx/xx GENETIC MAPPING FOR ONCOLOGY Conditions Melanoma Prostate Cancer
More informationGenetic association analysis incorporating intermediate phenotypes information for complex diseases
University of Iowa Iowa Research Online Theses and Dissertations Fall 2011 Genetic association analysis incorporating intermediate phenotypes information for complex diseases Yafang Li University of Iowa
More information# For the GWAS stage, B-cell NHL cases which small numbers (N<20) were excluded from analysis.
Supplementary Table 1a. Subtype Breakdown of all analyzed samples Stage GWAS Singapore Validation 1 Guangzhou Validation 2 Guangzhou Validation 3 Beijing Total No. of B-Cell Cases 253 # 168^ 294^ 713^
More informationComplex Multifactorial Genetic Diseases
Complex Multifactorial Genetic Diseases Nicola J Camp, University of Utah, Utah, USA Aruna Bansal, University of Utah, Utah, USA Secondary article Article Contents. Introduction. Continuous Variation.
More informationSupplementary Figure 1: Features of IGLL5 Mutations in CLL: a) Representative IGV screenshot of first
Supplementary Figure 1: Features of IGLL5 Mutations in CLL: a) Representative IGV screenshot of first intron IGLL5 mutation depicting biallelic mutations. Red arrows highlight the presence of out of phase
More informationGenetics and Genomics in Medicine Chapter 8 Questions
Genetics and Genomics in Medicine Chapter 8 Questions Linkage Analysis Question Question 8.1 Affected members of the pedigree above have an autosomal dominant disorder, and cytogenetic analyses using conventional
More information5/2/18. After this class students should be able to: Stephanie Moon, Ph.D. - GWAS. How do we distinguish Mendelian from non-mendelian traits?
corebio II - genetics: WED 25 April 2018. 2018 Stephanie Moon, Ph.D. - GWAS After this class students should be able to: 1. Compare and contrast methods used to discover the genetic basis of traits or
More informationGenetics of COPD Prof. Ian P Hall
Genetics of COPD 1 Prof. Ian P. Hall Dean, Faculty of Medicine and Health Sciences The University of Nottingham Medical School Ian.Hall@nottingham.ac.uk Chronic obstructive pulmonary disease (COPD) 900,000
More informationEtiology of Chronic Diseases. Complex Diseases Genes and Environment Initiative
Etiology of Chronic Diseases Complex Diseases Genes and Environment Initiative Top 10 Causes of Mortality in 2003 Death Rate per 100,000 Heart disease...232 Cancer...190 Cerebrovascular disease....54 Chronic
More informationLeveraging the Exome Sequencing Project: Creating a WHI Resource Through Exome Imputation in SHARe. Chris Carlson on behalf of WHISP May 5, 2011
Leveraging the Exome Sequencing Project: Creating a WHI Resource Through Exome Imputation in SHARe Chris Carlson on behalf of WHISP May 5, 2011 Exome Sequencing Project (ESP) Three cohort-based groups
More informationHaplotype allelic classes in the lactase persistence locus
Haplotype allelic classes in the lactase persistence locus Robert Cedergren Colloquium november 3 rd 28 Julie Hussin 1,2, Philippe Nadeau 1,2, Jean-François Lefebvre 2 and Damian Labuda 1-3 1 Bioinformatics
More informationGenomic structural variation
Genomic structural variation Mario Cáceres The new genomic variation DNA sequence differs across individuals much more than researchers had suspected through structural changes A huge amount of structural
More informationDrug Metabolism Disposition
Drug Metabolism Disposition The CYP2C19 intron 2 branch point SNP is the ancestral polymorphism contributing to the poor metabolizer phenotype in livers with CYP2C19*35 and CYP2C19*2 alleles Amarjit S.
More informationCOMPUTATIONAL OPTIMISATION OF TARGETED DNA SEQUENCING FOR CANCER DETECTION
COMPUTATIONAL OPTIMISATION OF TARGETED DNA SEQUENCING FOR CANCER DETECTION Pierre Martinez, Nicholas McGranahan, Nicolai Juul Birkbak, Marco Gerlinger, Charles Swanton* SUPPLEMENTARY INFORMATION SUPPLEMENTARY
More informationInvestigating causality in the association between 25(OH)D and schizophrenia
Investigating causality in the association between 25(OH)D and schizophrenia Amy E. Taylor PhD 1,2,3, Stephen Burgess PhD 1,4, Jennifer J. Ware PhD 1,2,5, Suzanne H. Gage PhD 1,2,3, SUNLIGHT consortium,
More informationQTL detection for traits of interest for the dairy goat industry
QTL detection for traits of interest for the dairy goat industry 64 th Annual Meeting EAAP 2013 26 th -30 th august Nantes, France C. Maroteau, I. Palhière, H. Larroque, V. Clément, G. Tosser-Klopp, R.
More informationNature Structural & Molecular Biology: doi: /nsmb.2419
Supplementary Figure 1 Mapped sequence reads and nucleosome occupancies. (a) Distribution of sequencing reads on the mouse reference genome for chromosome 14 as an example. The number of reads in a 1 Mb
More informationSupplementary Materials for
www.sciencetranslationalmedicine.org/cgi/content/full/7/283/283ra54/dc1 Supplementary Materials for Clonal status of actionable driver events and the timing of mutational processes in cancer evolution
More informationChallenges of CGH array testing in children with developmental delay. Dr Sally Davies 17 th September 2014
Challenges of CGH array testing in children with developmental delay Dr Sally Davies 17 th September 2014 CGH array What is CGH array? Understanding the test Benefits Results to expect Consent issues Ethical
More informationIntroduction to LOH and Allele Specific Copy Number User Forum
Introduction to LOH and Allele Specific Copy Number User Forum Jonathan Gerstenhaber Introduction to LOH and ASCN User Forum Contents 1. Loss of heterozygosity Analysis procedure Types of baselines 2.
More informationATHENA WISDOM INITIATIVE: RISK-BASED SCREENING FOR BREAST CANCER
ATHENA WISDOM INITIATIVE: RISK-BASED SCREENING FOR BREAST CANCER The Screening Debate in the US? ACS vs. USPSTF When to start, when to stop, screening intervals, modality] Little guidance around operationalizing
More informationUsing CART to Mine SELDI ProteinChip Data for Biomarkers and Disease Stratification
Using CART to Mine SELDI ProteinChip Data for Biomarkers and Disease Stratification Kenna Mawk, D.V.M. Informatics Product Manager Ciphergen Biosystems, Inc. Outline Introduction to ProteinChip Technology
More informationFONS Nové sekvenační technologie vklinickédiagnostice?
FONS 2010 Nové sekvenační technologie vklinickédiagnostice? Sekvenování amplikonů Sequence capture Celogenomové sekvenování FONS 2010 Sekvenování amplikonů Amplicon sequencing - amplicon sequencing enables
More informationHands-On Ten The BRCA1 Gene and Protein
Hands-On Ten The BRCA1 Gene and Protein Objective: To review transcription, translation, reading frames, mutations, and reading files from GenBank, and to review some of the bioinformatics tools, such
More informationSupplementary note: Comparison of deletion variants identified in this study and four earlier studies
Supplementary note: Comparison of deletion variants identified in this study and four earlier studies Here we compare the results of this study to potentially overlapping results from four earlier studies
More informationComplex Trait Genetics in Animal Models. Will Valdar Oxford University
Complex Trait Genetics in Animal Models Will Valdar Oxford University Mapping Genes for Quantitative Traits in Outbred Mice Will Valdar Oxford University What s so great about mice? Share ~99% of genes
More informationExploring the Importance of Single Nucleotide Polymorphisms of HSPA9 in DNA of Sarcoma Patients
University of New Hampshire University of New Hampshire Scholars' Repository Honors Theses and Capstones Student Scholarship Summer 2013 Exploring the Importance of Single Nucleotide Polymorphisms of HSPA9
More informationProblem 3: Simulated Rheumatoid Arthritis Data
Problem 3: Simulated Rheumatoid Arthritis Data Michael B Miller Michael Li Gregg Lind Soon-Young Jang The plan
More informationindicated in shaded lowercase letters (hg19, Chr2: 217,955, ,957,266).
Legend for Supplementary Figures Figure S1: Sequence of 2q35 encnv. The DNA sequence of the 1,375bp 2q35 encnv is indicated in shaded lowercase letters (hg19, Chr2: 217,955,892-217,957,266). Figure S2:
More informationAssessing Your Patient s Breast Cancer Risk: Is Genetic Testing Necessary?
May 16, 2016 Assessing Your Patient s Breast Cancer Risk: Is Genetic Testing Necessary? Presenter: Emily Kuchinsky, MS, CGC 1 Experiences with Genetic Testing Adverse Events in Cancer Genetic Testing:
More informationADVANCED PGT SERVICES
Genomic Prediction ADVANCED PGT SERVICES with PGT-A using SEQ is a cost-effective, rigorously validated, unambiguous, and streamlined test for aneuploidy in blastocyst biopsies, and uses state of the art
More informationPrecision Medicine and Genetic Counseling : Is Yes always the correct answer?
Precision Medicine and Genetic Counseling : Is Yes always the correct answer? Beverly M. Yashar, MS, PhD, CGC Director, Graduate Program in Genetic Counseling Professor, Department of Human Genetics. (yashar@umich.edu)
More informationSupplementary information for: A functional variation in BRAP confers risk of myocardial infarction in Asian populations
Supplementary information for: A functional variation in BRAP confers risk of myocardial infarction in Asian populations Kouichi Ozaki 1, Hiroshi Sato 2, Katsumi Inoue 3, Tatsuhiko Tsunoda 4, Yasuhiko
More informationSCALPEL MICRO-ASSEMBLY APPROACH TO DETECT INDELS WITHIN EXOME-CAPTURE DATA. Giuseppe Narzisi, PhD Schatz Lab
SCALPEL MICRO-ASSEMBLY APPROACH TO DETECT INDELS WITHIN EXOME-CAPTURE DATA Giuseppe Narzisi, PhD Schatz Lab November 14, 2013 Micro-Assembly Approach to detect INDELs 2 Outline Scalpel micro-assembly pipeline
More informationGenetic Testing: who, what, why?
Genetic Testing: who, what, why? Gina Westhoff MD LMG Gynecologic Oncology March 16, 2019 Disclosures Speaker for Merck (unrelated to today s topic) Objectives Determine who should undergo genetic risk
More informationSupplementary Figure 1. A - MSH6 p.val282thrfs*10: Endome. Endome. Colon
Supplementary Figure 1 - MSH6 p.val282hrfs*10: 1780 1785 C C C C C 1 B - MSH6 p.phe1088leufs*5: 1820 1810 Rectal Rectal Gastric C C C C C C Rectal C 2 C - MSH6 p.rg1172lysfs*5: 1745 1740 Ovarian 3 D -
More informationbreast cancer; relative risk; risk factor; standard deviation; strength of association
American Journal of Epidemiology The Author 2015. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail:
More informationSummary. Introduction. Atypical and Duplicated Samples. Atypical Samples. Noah A. Rosenberg
doi: 10.1111/j.1469-1809.2006.00285.x Standardized Subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, Accounting for Atypical and Duplicated Samples and Pairs of Close Relatives Noah A. Rosenberg
More informationARTICLE Identification of Susceptibility Genes for Cancer in a Genome-wide Scan: Results from the Colon Neoplasia Sibling Study
ARTICLE Identification of Susceptibility Genes for Cancer in a Genome-wide Scan: Results from the Colon Neoplasia Sibling Study Denise Daley, 1,9, * Susan Lewis, 2 Petra Platzer, 3,8 Melissa MacMillen,
More informationCancer Treatment and Research
Cancer Treatment and Research Volume 155 Series Editor Steven T. Rosen For further volumes: http://www.springer.com/series/5808 Boris Pasche Editor Cancer Genetics 123 Editor Boris Pasche, MD, PhD, FACP
More informationWhat is New in Genetic Testing. Steven D. Shapiro MS, DMD, MD
What is New in Genetic Testing Steven D. Shapiro MS, DMD, MD 18th Annual Primary Care Symposium Financial and Commercial Disclosure I have a no financial or commercial interest in my presentation. 2 Genetic
More information2) Cases and controls were genotyped on different platforms. The comparability of the platforms should be discussed.
Reviewers' Comments: Reviewer #1 (Remarks to the Author) The manuscript titled 'Association of variations in HLA-class II and other loci with susceptibility to lung adenocarcinoma with EGFR mutation' evaluated
More informationOvarian cancer variant rs is associated with HOXD1 and HOXD3 gene expression
/, 2017, Vol. 8, (No. 61), pp: 103410-103414 Ovarian cancer variant rs2072590 is associated with HOXD1 and HOXD3 gene expression Liyuan Guo 1,*, Yan Peng 2,*, Lei Sun 3,*, Xia Han 4, Juan Xu 4 and Dongwei
More informationMendelian Randomization
Mendelian Randomization Drawback with observational studies Risk factor X Y Outcome Risk factor X? Y Outcome C (Unobserved) Confounders The power of genetics Intermediate phenotype (risk factor) Genetic
More informationVariant Classification. Author: Mike Thiesen, Golden Helix, Inc.
Variant Classification Author: Mike Thiesen, Golden Helix, Inc. Overview Sequencing pipelines are able to identify rare variants not found in catalogs such as dbsnp. As a result, variants in these datasets
More information