Genome-wide copy-number calling (CNAs not CNVs!) Dr Geoff Macintyre
|
|
- Regina Manning
- 5 years ago
- Views:
Transcription
1 Genome-wide copy-number calling (CNAs not CNVs!) Dr Geoff Macintyre
2 Structural variation (SVs) Copy-number variations C Deletion A B C Balanced rearrangements A B A B C B A C Duplication Inversion Causes Replication errors Retrotransposition Repair errors Recombination errors Translocation
3 Why is copy-number important? Ciriello et al (2015). Nature Genetics
4
5
6 The data Genome-wide SNP allele frequencies Some measure of the amount of DNA for a given locus (e.g. sequencing depth)
7 Array based detection of SNPs (hybridisation)
8 SNP calling using affymetrix arrays Nucleic Acids Res. 2006; 34(14): e doi: /nar/gkl475
9 Further reading on genotyping Birdseed: CRLMM: HaplotypeCaller and UnifiedGenotyper: Varscan: GWAS primer:
10 Basic workflow Quantify signal depth/intensity B-allele Segment genome Hidden Markov model Smoothing methods Call copy-number changes Threshold Cluster Probabilistic models
11 Quantify signal Segment genome Call copynumber The data: logr Sequencing: log 2 (depth) Array: R(θ) subject = normalised intensity of probes from sample R(θ) expected = normalised intensity of probes from control logr = log 2 (R(θ) observed /R(θ) expected )
12 logr of HCC1143 cell-line using affy SNP6
13 Quantify signal Segment genome Call copynumber logr/depth normalisation Different proportions of GC in each region can produce a bias in the read depth (wave artifact) We can fit a loess model and remove the effect. LS041 Sample (CNAnorm package) Copy Number ratio GC content
14 Quantify signal Segment genome Call copynumber The data: B-allele frequency θ A = intensity of probe for allele A AA AA AB AAB ABB BAF = θ A /(θ A + θ B ) BB BB
15 Quantify signal Segment genome Call copynumber BAF banding 1 band: Background noise (0 copies). 2 bands: {A,B}, {AA,BB}, or {AAA,BBB}, Copy numbers (0, j). 3 bands: {AA,AB,BB} or {AAAA,AABB,BBBB},... Copy numbers (i, j=i) 4 bands: {AAA, ABB, AAB, BBB} or {AAAA, ABBB, AAAB, BBBB} or {AAAAA, ABBBB, AAAAB, BBBBB}, Copy numbers (i, j)/ i < j
16 BAF of HCC1143 cell-line using affy SNP6
17 Quantify signal Segment genome Call copynumber Segmentation: Circular binary segmentation Olshen et al., It can be used with array and sequencing data Finds change points using a ttest under a permutation model. Bioconductor package DNAcopy.
18 Quantify signal Segment genome Call copynumber Segmentation: Hidden markov models
19 Quantify signal Segment genome Call copynumber Copy-number calling: threshold based Individual thresholds based on the variability of each sample:
20 Quantify signal Segment genome Call copynumber Copy-number calling: cluster based van de Wiel et al., 2007 (CGHCall Bioconductor package). The segmented means come from a mixture of six normal populations. The model is fit by EM algorithm. Classification reduced to 3 or 4 states. (Usually loss, gain, normal)
21 Relative copy-number profile (ovarian cancer)
22 Method: QDNAseq Scheinin I et al., 2014 (QDNAseq Bioconductor package). Divides genome into bins of equal size. Normalisation based on blacklisted regions, GC content,... Segmentation with DNAcopy. Optional calling with CGHcall.
23 Exercise 1
24 Problems: purity and heterogeneity
25 What are the effects on relative copy-number?
26 Absolute copy-number profile (ovarian cancer)
27 Method: Allele-Specific Copy number Analysis of Tumours (ASCAT) constant tumour fraction A-allele copy-number B-allele copy-number ploidy
28 Further reading on copy-number Methods for CN detection (array data): Tools for CN detection (sequence data): PennCNV, a package for CNV calling: Large scale analysis of CNAs in cancer:
29 Exercise 2
Statistical 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 informationIdentification of regions with common copy-number variations using SNP array
Identification of regions with common copy-number variations using SNP array Agus Salim Epidemiology and Public Health National University of Singapore Copy Number Variation (CNV) Copy number alteration
More informationUnderstanding DNA Copy Number Data
Understanding DNA Copy Number Data Adam B. Olshen Department of Epidemiology and Biostatistics Helen Diller Family Comprehensive Cancer Center University of California, San Francisco http://cc.ucsf.edu/people/olshena_adam.php
More informationPloidy and large-scale genomic instability consistently identify basal-like breast
Supplementary Data and Figures Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation Popova T, Manié E, Rieunier G, Caux-Moncoutier V,
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 informationDNA-seq Bioinformatics Analysis: Copy Number Variation
DNA-seq Bioinformatics Analysis: Copy Number Variation Elodie Girard elodie.girard@curie.fr U900 institut Curie, INSERM, Mines ParisTech, PSL Research University Paris, France NGS Applications 5C HiC DNA-seq
More informationNature Genetics: doi: /ng Supplementary Figure 1. PCA for ancestry in SNV data.
Supplementary Figure 1 PCA for ancestry in SNV data. (a) EIGENSTRAT principal-component analysis (PCA) of SNV genotype data on all samples. (b) PCA of only proband SNV genotype data. (c) PCA of SNV genotype
More informationModeling genetic inheritance of copy number variations
Published online 2 October 2008 Nucleic Acids Research, 2008, Vol. 36, No. 21 e138 doi:10.1093/nar/gkn641 Modeling genetic inheritance of copy number variations Kai Wang 1,2, *, Zhen Chen 3, Mahlet G.
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 informationBACOM2: a Java tool for detecting normal cell contamination of copy number in heterogeneous tumor
Page 1 BACOM2: a Java tool for detecting normal cell contamination of copy number in heterogeneous tumor Yi Fu 1, Jun Ruan 2, Guoqiang Yu 1, Douglas A. Levine 3, Niya Wang 1, Ie- Ming Shih 4, Zhen Zhang
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 informationCopy Number Variations and Association Mapping Advanced Topics in Computa8onal Genomics
Copy Number Variations and Association Mapping 02-715 Advanced Topics in Computa8onal Genomics SNP and CNV Genotyping SNP genotyping assumes two copy numbers at each locus (i.e., no CNVs) CNV genotyping
More informationThe Loss of Heterozygosity (LOH) Algorithm in Genotyping Console 2.0
The Loss of Heterozygosity (LOH) Algorithm in Genotyping Console 2.0 Introduction Loss of erozygosity (LOH) represents the loss of allelic differences. The SNP markers on the SNP Array 6.0 can be used
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 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 informationCNV Detection and Interpretation in Genomic Data
CNV Detection and Interpretation in Genomic Data Benjamin W. Darbro, M.D., Ph.D. Assistant Professor of Pediatrics Director of the Shivanand R. Patil Cytogenetics and Molecular Laboratory Overview What
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 informationDetection of aneuploidy in a single cell using the Ion ReproSeq PGS View Kit
APPLICATION NOTE Ion PGM System Detection of aneuploidy in a single cell using the Ion ReproSeq PGS View Kit Key findings The Ion PGM System, in concert with the Ion ReproSeq PGS View Kit and Ion Reporter
More informationMosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer
Supplementary Information Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer Lars A. Forsberg, Chiara Rasi, Niklas Malmqvist, Hanna Davies, Saichand
More informationPSSV User Manual (V2.1)
PSSV User Manual (V2.1) 1. Introduction A novel pattern-based probabilistic approach, PSSV, is developed to identify somatic structural variations from WGS data. Specifically, discordant and concordant
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 informationGenetic Association Testing of Copy Number Variation
University of Kentucky UKnowledge Theses and Dissertations--Statistics Statistics 2014 Genetic Association Testing of Copy Number Variation Yinglei Li University of Kentucky, yinglei2014@gmail.com Click
More informationMultiple Copy Number Variations in a Patient with Developmental Delay ASCLS- March 31, 2016
Multiple Copy Number Variations in a Patient with Developmental Delay ASCLS- March 31, 2016 Marwan Tayeh, PhD, FACMG Director, MMGL Molecular Genetics Assistant Professor of Pediatrics Department of Pediatrics
More informationClinical evaluation of microarray data
Clinical evaluation of microarray data David Amor 19 th June 2011 Single base change Microarrays 3-4Mb What is a microarray? Up to 10 6 bits of Information!! Highly multiplexed FISH hybridisations. Microarray
More informationLTA Analysis of HapMap Genotype Data
LTA Analysis of HapMap Genotype Data Introduction. This supplement to Global variation in copy number in the human genome, by Redon et al., describes the details of the LTA analysis used to screen HapMap
More informationcn.mops - Mixture of Poissons for CNV detection in NGS data Günter Klambauer Institute of Bioinformatics, Johannes Kepler University Linz
Software Manual Institute of Bioinformatics, Johannes Kepler University Linz cn.mops - Mixture of Poissons for CNV detection in NGS data Günter Klambauer Institute of Bioinformatics, Johannes Kepler University
More informationTutorial: acgh Data Analysis With Chipster
Tutorial: acgh Data Analysis With Chipster Ilari Scheinin (firstname.lastname@gmail.com) January 14, 2011 Abstract This tutorial covers analysis of array comparative genomic hybridization (acgh) data with
More informationPSSV User Manual (V1.0)
PSSV User Manual (V1.0) 1. Introduction A novel pattern-based probabilistic approach, PSSV, is developed to identify somatic structural variations from WGS data. Specifically, discordant and concordant
More informationAbstract. Optimization strategy of Copy Number Variant calling using Multiplicom solutions APPLICATION NOTE. Introduction
Optimization strategy of Copy Number Variant calling using Multiplicom solutions Michael Vyverman, PhD; Laura Standaert, PhD and Wouter Bossuyt, PhD Abstract Copy number variations (CNVs) represent a significant
More informationUsing GWAS Data to Identify Copy Number Variants Contributing to Common Complex Diseases
arxiv:1010.5040v1 [stat.me] 25 Oct 2010 Statistical Science 2009, Vol. 24, No. 4, 530 546 DOI: 10.1214/09-STS304 c Institute of Mathematical Statistics, 2009 Using GWAS Data to Identify Copy Number Variants
More informationComputational Analysis of Genome-Wide DNA Copy Number Changes
Computational Analysis of Genome-Wide DNA Copy Number Changes Lei Song Thesis submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements
More informationClinical Genomics. Ina E. Amarillo, PhD FACMGG
Clinical Genomics Ina E. Amarillo, PhD FACMGG Associate Medical Director, Cytogenetics Lab (CaTG), Lab and Genomic Medicine Assistant Professor, Pathology and Immunology Outline Clinical Genomics Testing
More informationcn.mops - Mixture of Poissons for CNV detection in NGS data Günter Klambauer Institute of Bioinformatics, Johannes Kepler University Linz
Software Manual Institute of Bioinformatics, Johannes Kepler University Linz cn.mops - Mixture of Poissons for CNV detection in NGS data Günter Klambauer Institute of Bioinformatics, Johannes Kepler University
More informationCopy Number Varia/on Detec/on. Alex Mawla UCD Genome Center Bioinforma5cs Core Tuesday June 16, 2015
Copy Number Varia/on Detec/on Alex Mawla UCD Genome Center Bioinforma5cs Core Tuesday June 16, 2015 Today s Goals Understand the applica5on and capabili5es of using targe5ng sequencing and CNV calling
More informationcnvhap: an integrative population and haplotype based multiplatform model of SNPs and CNVs
cnvhap: an integrative population and haplotype based multiplatform model of SNPs and CNVs Lachlan J M Coin 1, Julian E Asher, Robin G Walters, Julia S El-Sayed Moustafa, Adam J de Smith, Rob Sladek 3,
More informationCNV detection. Introduction and detection in NGS data. G. Demidov 1,2. NGSchool2016. Centre for Genomic Regulation. CNV detection. G.
Introduction and detection in NGS data 1,2 1 Genomic and Epigenomic Variation in Disease group, Centre for Genomic Regulation 2 Universitat Pompeu Fabra NGSchool2016 methods: methods Outline methods: methods
More informationAnalysis of acgh data: statistical models and computational challenges
: statistical models and computational challenges Ramón Díaz-Uriarte 2007-02-13 Díaz-Uriarte, R. acgh analysis: models and computation 2007-02-13 1 / 38 Outline 1 Introduction Alternative approaches What
More informationBin Liu, Lei Yang, Binfang Huang, Mei Cheng, Hui Wang, Yinyan Li, Dongsheng Huang, Jian Zheng,
The American Journal of Human Genetics, Volume 91 Supplemental Data A Functional Copy-Number Variation in MAPKAPK2 Predicts Risk and Survival of Lung Cancer Bin Liu, Lei Yang, Binfang Huang, Mei Cheng,
More informationChromosome Structure & Recombination
Chromosome Structure & Recombination (CHAPTER 8- Brooker Text) April 4 & 9, 2007 BIO 184 Dr. Tom Peavy Genetic variation refers to differences between members of the same species or those of different
More informationSubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization
Qiao et al. Genome Biology 2014, 15:443 METHOD Open Access SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization Yi Qiao
More informationAssessment of Breast Cancer with Borderline HER2 Status Using MIP Microarray
Assessment of Breast Cancer with Borderline HER2 Status Using MIP Microarray Hui Chen, Aysegul A Sahin, Xinyan Lu, Lei Huo, Rajesh R Singh, Ronald Abraham, Shumaila Virani, Bal Mukund Mishra, Russell Broaddus,
More informationA general framework for analyzing tumor subclonality using SNP array and DNA sequencing data
Li and Li Genome Biology 2014, 15:473 METHOD A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data Bo Li 1 and Jun Z Li 2 Open Access Abstract Intra-tumor heterogeneity
More informationHuman Cancer Genome Project. Bioinformatics/Genomics of Cancer:
Bioinformatics/Genomics of Cancer: Professor of Computer Science, Mathematics and Cell Biology Courant Institute, NYU School of Medicine, Tata Institute of Fundamental Research, and Mt. Sinai School of
More informationSystematic Analysis for Identification of Genes Impacting Cancers
Systematic Analysis for Identification of Genes Impacting Cancers Arpita Singhal Stanford University Saint Francis High School ABSTRACT Currently, vast amounts of molecular information involving genomic
More informationComparing CNV detection methods for SNP arrays Laura Winchester, Christopher Yau and Jiannis Ragoussis
BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS. VOL 8. NO 5. 353^366 doi:10.1093/bfgp/elp017 Comparing CNV detection methods for SNP arrays Laura Winchester, Christopher Yau and Jiannis Ragoussis Advance
More informationComparison of segmentation methods in cancer samples
fig/logolille2. Comparison of segmentation methods in cancer samples Morgane Pierre-Jean, Guillem Rigaill, Pierre Neuvial Laboratoire Statistique et Génome Université d Évry Val d Éssonne UMR CNRS 8071
More informationOptimizing Copy Number Variation Analysis Using Genome-wide Short Sequence Oligonucleotide Arrays
Optimizing Copy Number Variation Analysis Using Genome-wide Short Sequence Oligonucleotide Arrays The Harvard community has made this article openly available. Please share how this access benefits you.
More informationSeven cases of intellectual disability analysed by genomewide SNP analysis. Rodney J. Scott
Seven cases of intellectual disability analysed by genomewide SNP analysis Rodney J. Scott Ability to interrogate Genomic Material ~1930 Crude analyses 2012 Highly precise analyses A (very) brief history
More informationStructural Variants and Susceptibility to Common Human Disorders Dr. Xavier Estivill
Structural Variants and Susceptibility Genetic Causes of Disease Lab Genes and Disease Program Center for Genomic Regulation (CRG) Barcelona 1 Complex genetic diseases Changes in prevalence (>10 fold)
More informationComparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays
Published online 8 February 2010 Nucleic Acids Research, 2010, Vol. 38, No. 9 e105 doi:10.1093/nar/gkq040 Comparative analyses of seven algorithms for copy number variant identification from single nucleotide
More informationSTATISTICAL METHODS FOR THE DETECTION AND ANALYSES OF STRUCTURAL VARIANTS IN THE HUMAN GENOME. Shu Mei, Teo
Department of Medical Epidemiology and Biostatistics Karolinska Institutet, Stockholm, Sweden & Saw Swee Hock School of Public Health National University of Singapore, Singapore STATISTICAL METHODS FOR
More informationAnalysis of CGH and SNP arrays for the detection of chromosomal aberrations in single cells
Analysis of CGH and SNP arrays for the detection of chromosomal aberrations in single cells Peter Konings 1 Evelyne Vanneste 1,2 Thierry Voet 1 Cédric Le Caignec 1 Michèle Ampe 1 Cindy Melotte 1 Sophie
More informationStructural Variation and Medical Genomics
Structural Variation and Medical Genomics Andrew King Department of Biomedical Informatics July 8, 2014 You already know about small scale genetic mutations Single nucleotide polymorphism (SNPs) Deletions,
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 informationSNP Array NOTE: THIS IS A SAMPLE REPORT AND MAY NOT REFLECT ACTUAL PATIENT DATA. FORMAT AND/OR CONTENT MAY BE UPDATED PERIODICALLY.
SAMPLE REPORT SNP Array NOTE: THIS IS A SAMPLE REPORT AND MAY NOT REFLECT ACTUAL PATIENT DATA. FORMAT AND/OR CONTENT MAY BE UPDATED PERIODICALLY. RESULTS SNP Array Copy Number Variations Result: GAIN,
More informationNature Genetics: doi: /ng Supplementary Figure 1. Mutational signatures in BCC compared to melanoma.
Supplementary Figure 1 Mutational signatures in BCC compared to melanoma. (a) The effect of transcription-coupled repair as a function of gene expression in BCC. Tumor type specific gene expression levels
More informationContents. 1.5 GOPredict is robust to changes in study sets... 5
Supplementary documentation for Data integration to prioritize drugs using genomics and curated data Riku Louhimo, Marko Laakso, Denis Belitskin, Juha Klefström, Rainer Lehtonen and Sampsa Hautaniemi Faculty
More informationSupplementary Figure 1. Schematic diagram of o2n-seq. Double-stranded DNA was sheared, end-repaired, and underwent A-tailing by standard protocols.
Supplementary Figure 1. Schematic diagram of o2n-seq. Double-stranded DNA was sheared, end-repaired, and underwent A-tailing by standard protocols. A-tailed DNA was ligated to T-tailed dutp adapters, circularized
More informationIntroduction to Genetics
Introduction to Genetics Table of contents Chromosome DNA Protein synthesis Mutation Genetic disorder Relationship between genes and cancer Genetic testing Technical concern 2 All living organisms consist
More informationNext Generation Sequencing as a tool for breakpoint analysis in rearrangements of the globin-gene clusters
Next Generation Sequencing as a tool for breakpoint analysis in rearrangements of the globin-gene clusters XXXth International Symposium on Technical Innovations in Laboratory Hematology Honolulu, Hawaii
More informationCURRENT GENETIC TESTING TOOLS IN NEONATAL MEDICINE. Dr. Bahar Naghavi
2 CURRENT GENETIC TESTING TOOLS IN NEONATAL MEDICINE Dr. Bahar Naghavi Assistant professor of Basic Science Department, Shahid Beheshti University of Medical Sciences, Tehran,Iran 3 Introduction Over 4000
More informationOncoPhase: Quantification of somatic mutation cellular prevalence using phase information
OncoPhase: Quantification of somatic mutation cellular prevalence using phase information Donatien Chedom-Fotso 1, 2, 3, Ahmed Ashour Ahmed 1, 2, and Christopher Yau 3, 4 1 Ovarian Cancer Cell Laboratory,
More informationSNP Array NOTE: THIS IS A SAMPLE REPORT AND MAY NOT REFLECT ACTUAL PATIENT DATA. FORMAT AND/OR CONTENT MAY BE UPDATED PERIODICALLY.
SAMPLE REPORT SNP Array NOTE: THIS IS A SAMPLE REPORT AND MAY NOT REFLECT ACTUAL PATIENT DATA. FORMAT AND/OR CONTENT MAY BE UPDATED PERIODICALLY. RESULTS SNP Array Copy Number Variations Result: LOSS,
More informationNature Biotechnology: doi: /nbt.1904
Supplementary Information Comparison between assembly-based SV calls and array CGH results Genome-wide array assessment of copy number changes, such as array comparative genomic hybridization (acgh), is
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 informationIntegration of microarray analysis into the clinical diagnosis of hematological malignancies: How much can we improve cytogenetic testing?
/, Vol. 6, No. 22 Integration of microarray analysis into the clinical diagnosis of hematological malignancies: How much can we improve cytogenetic testing? Jess F. Peterson 1,2,6, Nidhi Aggarwal 3, Clayton
More informationBiology 105: Introduction to Genetics Midterm EXAM. Part1. Definitions. 1 Recessive allele. Name. Student ID. 2 Homologous chromosomes
Biology 105: Introduction to Genetics Midterm EXAM Part1 Definitions 1 Recessive allele Name Student ID 2 Homologous chromosomes Before starting, write your name on the top of each page Make sure you have
More informationAnalysis of Somatic Alterations in Cancer Genome: From SNP Arrays to Next Generation Sequencing
Analysis of Somatic Alterations in Cancer Genome: From SNP Arrays to Next Generation Sequencing Tatiana Popova, Valentina Boeva, Elodie Manié, Yves Rozenholc, Emmanuel Barillot, Marc-Henri Stern To cite
More informationAssociating Copy Number and SNP Variation with Human Disease. Autism Segmental duplication Neurobehavioral, includes social disability
Technical Note Associating Copy Number and SNP Variation with Human Disease Abstract The Genome-Wide Human SNP Array 6.0 is an affordable tool to examine the role of copy number variation in disease by
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 informationGinkgo Interactive analysis and quality assessment of single-cell CNV data
Ginkgo Interactive analysis and quality assessment of single-cell CNV data @RobAboukhalil Robert Aboukhalil, Tyler Garvin, Jude Kendall, Timour Baslan, Gurinder S. Atwal, Jim Hicks, Michael Wigler, Michael
More information22q11.2 DELETION SYNDROME. Anna Mª Cueto González Clinical Geneticist Programa de Medicina Molecular y Genética Hospital Vall d Hebrón (Barcelona)
22q11.2 DELETION SYNDROME Anna Mª Cueto González Clinical Geneticist Programa de Medicina Molecular y Genética Hospital Vall d Hebrón (Barcelona) Genomic disorders GENOMICS DISORDERS refers to those diseases
More informationMutation Detection and CNV Analysis for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research
Mutation Detection and CNV Analysis for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research Application Note Authors John McGuigan, Megan Manion,
More informationCHROMOSOMAL MICROARRAY (CGH+SNP)
Chromosome imbalances are a significant cause of developmental delay, mental retardation, autism spectrum disorders, dysmorphic features and/or birth defects. The imbalance of genetic material may be due
More informationBiostatistical modelling in genomics for clinical cancer studies
This work was supported by Entente Cordiale Cancer Research Bursaries Biostatistical modelling in genomics for clinical cancer studies Philippe Broët JE 2492 Faculté de Médecine Paris-Sud In collaboration
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 informationCNV PCA Search Tutorial
CNV PCA Search Tutorial Release 8.1 Golden Helix, Inc. March 18, 2014 Contents 1. Data Preparation 2 A. Join Log Ratio Data with Phenotype Information.............................. 2 B. Activate only
More informationSUPPLEMENTARY INFORMATION
CONTENTS A. AUTISM SPECTRUM DISORDER (ASD) SAMPLE AND CONTROL COLLECTIONS 4 ASD samples 4 Control cohorts 4 B. GENOTYPING AND DATA CLEANING 6 SNP quality control 6 Intensity quality control for CNV detection
More informationSupplementary Figures
Supplementary Figures Supplementary Figure 1. Heatmap of GO terms for differentially expressed genes. The terms were hierarchically clustered using the GO term enrichment beta. Darker red, higher positive
More informationAbsolute quantification of somatic DNA alterations in human cancer
Absolute quantification of somatic DNA alterations in human cancer The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Citation
More informationCopy Number Variations
Copy Number Variations Illumina Seminar - Milan June 18, 2009 Untangling the complexity of mendelian and complex diseases Federica Torri Dept of Science & Biomedical Technologies Fondazione Filarete, University
More informationA novel and universal method for microrna RT-qPCR data normalization
A novel and universal method for microrna RT-qPCR data normalization Jo Vandesompele professor, Ghent University co-founder and CEO, Biogazelle 4 th International qpcr Symposium Weihenstephan, March 1,
More informationDETECTING HIGHLY DIFFERENTIATED COPY-NUMBER VARIANTS FROM POOLED POPULATION SEQUENCING
DETECTING HIGHLY DIFFERENTIATED COPY-NUMBER VARIANTS FROM POOLED POPULATION SEQUENCING DANIEL R. SCHRIDER * Department of Biology and School of Informatics and Computing, Indiana University, 1001 E Third
More informationRisk-prediction modelling in cancer with multiple genomic data sets: a Bayesian variable selection approach
Risk-prediction modelling in cancer with multiple genomic data sets: a Bayesian variable selection approach Manuela Zucknick Division of Biostatistics, German Cancer Research Center Biometry Workshop,
More informationMRC-Holland MLPA. Description version 18; 09 September 2015
SALSA MLPA probemix P090-A4 BRCA2 Lot A4-0715, A4-0714, A4-0314, A4-0813, A4-0712: Compared to lot A3-0710, the 88 and 96 nt control fragments have been replaced (QDX2). This product is identical to the
More informationSupplementary Information. Supplementary Figures
Supplementary Information Supplementary Figures.8 57 essential gene density 2 1.5 LTR insert frequency diversity DEL.5 DUP.5 INV.5 TRA 1 2 3 4 5 1 2 3 4 1 2 Supplementary Figure 1. Locations and minor
More informationBreast and ovarian cancer in Serbia: the importance of mutation detection in hereditary predisposition genes using NGS
Breast and ovarian cancer in Serbia: the importance of mutation detection in hereditary predisposition genes using NGS dr sc. Ana Krivokuća Laboratory for molecular genetics Institute for Oncology and
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 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 informationIntegration of Cancer Genome into GECCO- Genetics and Epidemiology of Colorectal Cancer Consortium
Integration of Cancer Genome into GECCO- Genetics and Epidemiology of Colorectal Cancer Consortium Ulrike Peters Fred Hutchinson Cancer Research Center University of Washington U01-CA137088-05, PI: Peters
More informationIntroduction to genetic variation. He Zhang Bioinformatics Core Facility 6/22/2016
Introduction to genetic variation He Zhang Bioinformatics Core Facility 6/22/2016 Outline Basic concepts of genetic variation Genetic variation in human populations Variation and genetic disorders Databases
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 information2008 WERS Certified Products Directory - NFRC
2008 WERS Certified Products Directory - NFRC NOTES 1. U w is the whole window U-value 2. SHGC w is the whole window solar heat gain coefficient www.wers.net 3. T vw is the whole window visible (light)
More informationNature Genetics: doi: /ng Supplementary Figure 1. Rates of different mutation types in CRC.
Supplementary Figure 1 Rates of different mutation types in CRC. (a) Stratification by mutation type indicates that C>T mutations occur at a significantly greater rate than other types. (b) As for the
More informationGenetic Testing 101: Interpreting the Chromosomes
Genetic Testing 101: Interpreting the Chromosomes Kristin Lindstrom, MD Division of Genetics and Metabolism Phoenix Children s Hospital AzAAP Pediatrics in the Red Rocks I have no disclosures for this
More informationNew: P077 BRCA2. This new probemix can be used to confirm results obtained with P045 BRCA2 probemix.
SALSA MLPA KIT P045-B2 BRCA2/CHEK2 Lot 0410, 0609. As compared to version B1, four reference probes have been replaced and extra control fragments at 100 and 105 nt (X/Y specific) have been included. New:
More informationarxiv: v4 [stat.me] 7 May 2010
Submitted to the Annals of Applied Statistics arxiv: 0906.2234 RECONSTRUCTING DNA COPY NUMBER BY PENALIZED ESTIMATION AND IMPUTATION arxiv:0906.2234v4 [stat.me] 7 May 2010 By Zhongyang Zhang, Kenneth Lange,
More informationUNIVERSITI TEKNOLOGI MARA COPY NUMBER VARIATIONS OF ORANG ASLI (NEGRITO) FROM PENINSULAR MALAYSIA
UNIVERSITI TEKNOLOGI MARA COPY NUMBER VARIATIONS OF ORANG ASLI (NEGRITO) FROM PENINSULAR MALAYSIA SITI SHUHADA MOKHTAR Thesis submitted in fulfillment of the requirements for the degree of Master of Science
More informationChapter 1 : Genetics 101
Chapter 1 : Genetics 101 Understanding the underlying concepts of human genetics and the role of genes, behavior, and the environment will be important to appropriately collecting and applying genetic
More informationLecture 6: Linkage analysis in medical genetics
Lecture 6: Linkage analysis in medical genetics Magnus Dehli Vigeland NORBIS course, 8 th 12 th of January 2018, Oslo Approaches to genetic mapping of disease Multifactorial disease Monogenic disease Syke
More information