NEXT GENERATION SEQUENCING. R. Piazza (MD, PhD) Dept. of Medicine and Surgery, University of Milano-Bicocca
|
|
|
- Valerie Walsh
- 5 years ago
- Views:
Transcription
1 NEXT GENERATION SEQUENCING R. Piazza (MD, PhD) Dept. of Medicine and Surgery, University of Milano-Bicocca
2 SANGER SEQUENCING Capillary Electrophoresis DNA
3 NEXT GENERATION SEQUENCING SOLEXA-ILLUMINA TECHNOLOGY Flowcell
4 NEXT-GEN SEQUENCING DNA LIBRARY Genomic DNA Single-Read Paired-End ~100bp ~100bp
5
6 NEXT GENERATION SEQUENCING Clusters At the end of the amplification step millions of double-stranded DNA clusters are generated in each lane of the flowcell
7 NEXT GENERATION SEQUENCING All 4 nucleotides are added together Sequencing Primer Blocked, fluorescent nucleotides
8 NEXT GENERATION SEQUENCING IMAGE ACQUISITION 3 BLOCK REMOVAL FLUOROPHORE REMOVAL
9 HIGH-THROUGHPUT SEQUENCING The sequence is read in each cluster through multiple cycles of nucleotide incorporation
10
11 NEXT GENERATION SEQUENCING
12 HiSeq Lane/Flowcell 2 FLOWCELLS 8 Lane/Flowcell 250 * 10^6 Cluster/Lane 250 * 10^6 Cluster/Lane 125bp 125bp 2 x 125bp/Cluster (Pair-end) Throughput = 2 * 8 * 250 * 10^6 * 2 * 125bp = bp!! = 1 Tb (Terabase)
13 SANGER SEQ vs. NGS THROUGHPUT COST Allele #1 Allele #2 C A G C G A C A G C A G C A T T G G G A C C A G C G A C A G C G G C A T T G G G A C Coverage = 5 NGS Read #5 NGS Read #4 NGS Read #3 NGS Read #2 NGS Read #1 Allele #1 Allele #2 C A G C G A C A G C G G C A T T G G G A C C A G C G A C A G C A G C A T T G G G A C C A G C G A C A G C A G C A T T G G G A C C A G C G A C A G C G G C A T T G G G A C C A G C G A C A G C G G C A T T G G G A C C A G C G A C A G C A G C A T T G G G A C C A G C G A C A G C G G C A T T G G G A C
14 HIGH-THROUGHPUT SEQUENCING: APPLICATIONS DNA RNA GENOMIC DNA SEQUENCING RESEQUENCING DE NOVO SEQUENCING WHOLE-EXOME SEQUENCING ChIP-Seq DEEP SEQUENCING METHYL-SEQ mrna SEQUENCING (RNA-Seq) TRANSCRIPTOME SEQUENCING (RNA-SEQ) TAG SEQUENCING (DITAG) MICRO-RNA STUDIES
15 WHOLE-GENOME, WHOLE-EXOME AND ULTRADEEP SEQUENCING COVERAGE COVERAGE WHOLE-GENOME ULTRADEEP-SEQ
16 WHOLE-GENOME SEQUENCING: WHY? BY USING WHOLE-GENOME SEQUENCING WE ARE ABLE TO SEQUENCE AN ENTIRE GENOME, LEADING TO AN ALMOST UNBIASED ANALYSIS OF ALL THE VARIANTS THAT ARE PRESENT IN THAT SAMPLE HOWEVER, SEQUENCING IS STILL VERY EXPENSIVE, ANALYSIS COMPLEX AND FINAL COVERAGE IS USUALLY LIMITED, WHICH MEANS THAT THERE COULD BE SEQUENCING HOLES (REGIONS WITH POOR OR NO COVERAGE)
17 ULTRADEEP SEQUENCING: WHY? SUBCLONAL MUTATIONS M M ABL kinase domain
18 SONICATION M M
19 WHOLE-EXOME SEQUENCING
20
21
22 SINGLE NUCLEOTIDE POLYMORPHISM VARIANT CALLING MUTATION OR SNP? SOMATIC VARIANT GACAGACTACAACAGCACTTCTGACCAAGC GGGACAGACAACAACAGAACTTCTGACCAA TGGGACAGACTACAACAGCACTTCTGACCA ATTGGGACAGACAACAACAGAACTTCTGAC GCATTGGGACAGACTACAACAGCACTTCTGA GGCATTGGGACAGACTACAACAGCACTTCTG GGCATTGGGACAGACAACAACAGAACTTCTG CGGCATTGGGACAGACAACAACAGAACTTCT..CGGCATTGGGACAGACAACAACAGCACTTCTGACCAAGCGGAGAAGAGCT.. CASE SAMPLE GACAGACAACAACAGCACTTCTGACCAAGC GGGACAGACAACAACAGCACTTCTGACCAA TGGGACAGACTACAACAGCACTTCTGACCA ATTGGGACAGACAACAACAGCACTTCTGAC GCATTGGGACAGACTACAACAGCACTTCTGA GGCATTGGGACAGACAACAACAGCACTTCTG CONTROL SAMPLE GGCATTGGGACAGACAACAACAGCACTTCTG CGGCATTGGGACAGACTACAACAGCACTTCT..CGGCATTGGGACAGACAACAACAGCACTTCTGACCAAGCGGAGAAGAGCT..
23
24 SOMATIC VARIANT: DRIVER OR PASSENGER?
25 CASE CONTROL DELETIONS? AMPLIFICATIONS?
26 CASE CONTROL LOSS OF HETEROZYGOSITY ALLELIC IMBALANCE A A T T A A T
27 WHOLE-EXOME SEQUENCING GOES DIGITAL: CEQer COMPARATIVE EXONIC QUANTIFICATION ANALYZER Piazza R. et al., PLoS One Oct 4;8(10):e74825
28 Statistical module Wilcoxon Signed-Rank test Test statistic W W N r ( case ) ( control ) sgn x x R i i i i 1 As sample size increases (Nr > 10) the Z-Score converges to a Gaussian distribution! Estimating the error function of the normal distribution of W.. Wilcoxon Signed-Rank test erf ( x )..using the Abramowitz and Stegun approximation equation a 1 t a 2 t 2 a 3 t 3 a 4 t 4 a 5 t 5 e x 2
29 SOMATIC VARIANTS DETECTION WHOLE-GENOME WHOLE-EXOME ULTRADEEP SEQ WHICH ONE?
30 CASE STUDY #1 PROF. X ASKS YOU TO DEVELOP A PROTOCOL IN ORDER TO IDENTIFY THE SOMATIC MUTATIONS RESPONSIBLE FOR A RARE TYPE OF CANCER TOTAL NUMBER OF MATCHED (TUMOR + GERMLINE) CASES AVAILABLE: 9 TOTAL NUMBER OF TUMOR-ONLY CASES (gdna) AVAILABLE: 30 DATA AVAILABLE IN LITERATURE: NONE
31 CASE STUDY #2 PROF. X ASKS YOU TO DEVELOP A PROTOCOL IN ORDER TO IDENTIFY THE SOMATIC MUTATIONS RESPONSIBLE FOR A COMMON TYPE OF CANCER TOTAL NUMBER OF MATCHED (TUMOR + GERMLINE) CASES AVAILABLE: 35 TOTAL NUMBER OF TUMOR-ONLY CASES (gdna) AVAILABLE: 160 DATA AVAILABLE IN LITERATURE: EXTENSIVE KNOWLEDGE OF A SET OF 6 SOMATIC VARIANTS RESPONSIBLE FOR 80-90%OF CASES
32 CASE STUDY #3 PROF. X ASKS YOU TO DEVELOP A PROTOCOL TO STUDY THE PRESENCE OF MINIMAL RESIDUAL DISEASE IN A LEUKEMIC PATIENT WHO UNDERWENT ALLOGENEIC BONE MARROW TRANSPLANTATION TOTAL NUMBER OF CASES AVAILABLE: 1 DATA AVAILABLE: SOMATIC MUTATIONS RESPONSIBLE FOR THE ONSET OF THE DISEASE ARE KNOWN
33 RNA-Seq LOW EXPRESSION HIGH EXPRESSION RNA-SEQ READ EXON EXON
34 TRASLOCAZIONI ONCOGENICHE
35 DETECTION OF ONCOGENIC FUSIONS EXOME SEQUENCING? FRAGMENTATION?
36 RNA-Seq DRIVER FUSION TRANSCRIPTS IDENTIFICATION Junction reads Bridge reads 76bp 76bp Piazza R. et al., Nucleic Acids Res Sep;40(16):e123
37 XVI-XVII secolo: anatomia umana XIX secolo: microbiologia XX secolo: biochimica e biologia molecolare : rivoluzione genetica
38
39 SOMATIC VARIANTS Time 0 P P P * Time 2 * * P P * * * P * * P P * P ** * P P = PASSENGER VARIANTS * = DRIVER VARIANT * = DRIVER VARIANT P * Time 1 P *
40 DNA POLIMERASI
41 LIBRO: 300 PAGINE 1500 CARATTERI PER PAGINA CARATTERI DNA POLIMERASI DNA GENOMICO UMANO: DI CARATTERI (BASI)! L EQUIVALENTE DI LIBRI!! TURN-OVER CELLULARE: MILIARDI DI CELLULE AL GIORNO LE DNA POLIMERASI DEVONO LEGGERE E COPIARE IN MEDIA 600 MILIARDI DI MILIARDI DI BASI AL GIORNO: OLTRE 1 MILIONE DI MILIARDI DI LIBRI AL GIORNO
42
43 Piazza R. et al., Recurrent SETBP1 mutations in atypical chronic myeloid leukemia. Nat Genet Jan;45(1):18-24 Gambacorti-Passerini C. et al., Recurrent ETNK1 mutations in atypical chronic myeloid leukemia. Blood Jan 15;125(3):
44 SUBCLONAL EVOLUTION - METHYLCELLULOSE ASSAY Methylcellulose Medium CLONES/PATIENT MATCHED EXOME SEQUENCING ULTRADEEP SEQUENCING TARGETED AMPLIFICATION
45 PATIENT CMLPh-019 Somatic Variants ETNK1 p.n244s SETBP1 p.g870s ASXL1 p.r412* CBL p.c384y Coordinates Chr12: , A/G Chr18: , G/A Chr20: , C/T Chr11: , G/A
46 PATIENT CMLPh-013 Somatic Variants ETNK1 p.n244s SETBP1 g.g870s ASXL1 g.y586* NRAS g.g12d Coordinates Chr12: , A/G Chr18: , G/A Chr20: , C/G Chr1: , C/T
Analysis 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
DNA-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
NGS in Cancer Pathology After the Microscope: From Nucleic Acid to Interpretation
NGS in Cancer Pathology After the Microscope: From Nucleic Acid to Interpretation Michael R. Rossi, PhD, FACMG Assistant Professor Division of Cancer Biology, Department of Radiation Oncology Department
NGS in tissue and liquid biopsy
NGS in tissue and liquid biopsy Ana Vivancos, PhD Referencias So, why NGS in the clinics? 2000 Sanger Sequencing (1977-) 2016 NGS (2006-) ABIPrism (Applied Biosystems) Up to 2304 per day (96 sequences
Multiplex target enrichment using DNA indexing for ultra-high throughput variant detection
Multiplex target enrichment using DNA indexing for ultra-high throughput variant detection Dr Elaine Kenny Neuropsychiatric Genetics Research Group Institute of Molecular Medicine Trinity College Dublin
AVENIO family of NGS oncology assays ctdna and Tumor Tissue Analysis Kits
AVENIO family of NGS oncology assays ctdna and Tumor Tissue Analysis Kits Accelerating clinical research Next-generation sequencing (NGS) has the ability to interrogate many different genes and detect
Please Silence Your Cell Phones. Thank You
Please Silence Your Cell Phones Thank You Utility of NGS and Comprehensive Genomic Profiling in Hematopathology Practice Maria E. Arcila M.D. Memorial Sloan Kettering Cancer Center New York, NY Disclosure
The lymphoma-associated NPM-ALK oncogene elicits a p16ink4a/prb-dependent tumor-suppressive pathway. Blood Jun 16;117(24):
DNA Sequencing Publications Standard Sequencing 1 Carro MS et al. DEK Expression is controlled by E2F and deregulated in diverse tumor types. Cell Cycle. 2006 Jun;5(11) 2 Lassandro L et al. The DNA sequence
Advance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library
Advance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library Marilou Wijdicks International Product Manager Research For Life Science Research Only. Not for Use in Diagnostic Procedures.
Reporting TP53 gene analysis results in CLL
Reporting TP53 gene analysis results in CLL Mutations in TP53 - From discovery to clinical practice in CLL Discovery Validation Clinical practice Variant diversity *Leroy at al, Cancer Research Review
Illumina Trusight Myeloid Panel validation A R FHAN R A FIQ
Illumina Trusight Myeloid Panel validation A R FHAN R A FIQ G E NETIC T E CHNOLOGIST MEDICAL G E NETICS, CARDIFF To Cover Background to the project Choice of panel Validation process Genes on panel, Protocol
Supplementary Figure 1. Estimation of tumour content
Supplementary Figure 1. Estimation of tumour content a, Approach used to estimate the tumour content in S13T1/T2, S6T1/T2, S3T1/T2 and S12T1/T2. Tissue and tumour areas were evaluated by two independent
Using the Bravo Liquid-Handling System for Next Generation Sequencing Sample Prep
Using the Bravo Liquid-Handling System for Next Generation Sequencing Sample Prep Tom Walsh, PhD Division of Medical Genetics University of Washington Next generation sequencing Sanger sequencing gold
CRISPR/Cas9 Enrichment and Long-read WGS for Structural Variant Discovery
CRISPR/Cas9 Enrichment and Long-read WGS for Structural Variant Discovery PacBio CoLab Session October 20, 2017 For Research Use Only. Not for use in diagnostics procedures. Copyright 2017 by Pacific Biosciences
genomics for systems biology / ISB2020 RNA sequencing (RNA-seq)
RNA sequencing (RNA-seq) Module Outline MO 13-Mar-2017 RNA sequencing: Introduction 1 WE 15-Mar-2017 RNA sequencing: Introduction 2 MO 20-Mar-2017 Paper: PMID 25954002: Human genomics. The human transcriptome
Molecular Markers. Marcie Riches, MD, MS Associate Professor University of North Carolina Scientific Director, Infection and Immune Reconstitution WC
Molecular Markers Marcie Riches, MD, MS Associate Professor University of North Carolina Scientific Director, Infection and Immune Reconstitution WC Overview Testing methods Rationale for molecular testing
Rapid genomic screening of embryos using nanopore sequencing
Rapid genomic screening of embryos using nanopore sequencing Daniel J Turner, PhD Senior Director of Applications Oxford Nanopore Technologies Forman EJ & Scott RT Jr Contemporary OB/GYN () 2014 Euploid
Supplementary 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
R. Piazza (MD, PhD), Dept. of Medicine and Surgery, University of Milano-Bicocca EPIGENETICS
R. Piazza (MD, PhD), Dept. of Medicine and Surgery, University of Milano-Bicocca EPIGENETICS EPIGENETICS THE STUDY OF CHANGES IN GENE EXPRESSION THAT ARE POTENTIALLY HERITABLE AND THAT DO NOT ENTAIL A
AD (Leave blank) TITLE: Genomic Characterization of Brain Metastasis in Non-Small Cell Lung Cancer Patients
AD (Leave blank) Award Number: W81XWH-12-1-0444 TITLE: Genomic Characterization of Brain Metastasis in Non-Small Cell Lung Cancer Patients PRINCIPAL INVESTIGATOR: Mark A. Watson, MD PhD CONTRACTING ORGANIZATION:
Laboratory Service Report
Client C7028846-DLP Rochester Rochester, N 55901 Specimen Type Peripheral blood CR PDF Report available at: https://test.mmlaccess.com/reports/c7028846-zwselwql7p.ashx Indication for Test DS CR Pathogenic
The feasibility of circulating tumour DNA as an alternative to biopsy for mutational characterization in Stage III melanoma patients
The feasibility of circulating tumour DNA as an alternative to biopsy for mutational characterization in Stage III melanoma patients ASSC Scientific Meeting 13 th October 2016 Prof Andrew Barbour UQ SOM
Whole Genome and Transcriptome Analysis of Anaplastic Meningioma. Patrick Tarpey Cancer Genome Project Wellcome Trust Sanger Institute
Whole Genome and Transcriptome Analysis of Anaplastic Meningioma Patrick Tarpey Cancer Genome Project Wellcome Trust Sanger Institute Outline Anaplastic meningioma compared to other cancers Whole genomes
Spectrum of somatically acquired mutations identified by combining WES and genome-wide DNA array analysis in the discovery cohort of 30 JMML cases.
Supplementary Figure 1 Spectrum of somatically acquired mutations identified by combining WES and genome-wide DNA array analysis in the discovery cohort of 30 JMML cases. A total of 85 somatically acquired
TCF3 breakpoints of TCF3-PBX1 (patients 1a 5a) and TCF3-HLF (patients 6a 9a and11a) translocations.
Supplementary Figure 1 TCF3 breakpoints of TCF3-PBX1 (patients 1a 5a) and TCF3-HLF (patients 6a 9a and11a) translocations. The CpG motifs closest to the breakpoints are highlighted in red boxes and the
of TERT, MLL4, CCNE1, SENP5, and ROCK1 on tumor development were discussed.
Supplementary Note The potential association and implications of HBV integration at known and putative cancer genes of TERT, MLL4, CCNE1, SENP5, and ROCK1 on tumor development were discussed. Human telomerase
Disclosure. Summary. Circulating DNA and NGS technology 3/27/2017. Disclosure of Relevant Financial Relationships. JS Reis-Filho, MD, PhD, FRCPath
Circulating DNA and NGS technology JS Reis-Filho, MD, PhD, FRCPath Director of Experimental Pathology, Department of Pathology Affiliate Member, Human Oncology and Pathogenesis Program Disclosure of Relevant
Cytogenetics 101: Clinical Research and Molecular Genetic Technologies
Cytogenetics 101: Clinical Research and Molecular Genetic Technologies Topics for Today s Presentation 1 Classical vs Molecular Cytogenetics 2 What acgh? 3 What is FISH? 4 What is NGS? 5 How can these
Laboratory Service Report
Specimen Type Peripheral blood CR PDF Report available at: https://test.mmlaccess.com/reports/c7028846-ih2xuglwpq.ashx Indication for Test DS CR Pathogenic utations Detected CR 1. JAK2: c.1849g>t;p.val617phe
Genomic tests to personalize therapy of metastatic breast cancers. Fabrice ANDRE Gustave Roussy Villejuif, France
Genomic tests to personalize therapy of metastatic breast cancers Fabrice ANDRE Gustave Roussy Villejuif, France Future application of genomics: Understand the biology at the individual scale Patients
Research Strategy: 1. Background and Significance
Research Strategy: 1. Background and Significance 1.1. Heterogeneity is a common feature of cancer. A better understanding of this heterogeneity may present therapeutic opportunities: Intratumor heterogeneity
Characterisation of structural variation in breast. cancer genomes using paired-end sequencing on. the Illumina Genome Analyser
Characterisation of structural variation in breast cancer genomes using paired-end sequencing on the Illumina Genome Analyser Phil Stephens Cancer Genome Project Why is it important to study cancer? Why
Clonal Evolution of saml. Johnnie J. Orozco Hematology Fellows Conference May 11, 2012
Clonal Evolution of saml Johnnie J. Orozco Hematology Fellows Conference May 11, 2012 CML: *bcr-abl and imatinib Melanoma: *braf and vemurafenib CRC: *k-ras and cetuximab Esophageal/Gastric: *Her-2/neu
RNA SEQUENCING AND DATA ANALYSIS
RNA SEQUENCING AND DATA ANALYSIS Length of mrna transcripts in the human genome 5,000 5,000 4,000 3,000 2,000 4,000 1,000 0 0 200 400 600 800 3,000 2,000 1,000 0 0 2,000 4,000 6,000 8,000 10,000 Length
Accessing and Using ENCODE Data Dr. Peggy J. Farnham
1 William M Keck Professor of Biochemistry Keck School of Medicine University of Southern California How many human genes are encoded in our 3x10 9 bp? C. elegans (worm) 959 cells and 1x10 8 bp 20,000
Next generation diagnostics Bringing high-throughput sequencing into clinical application
Next generation diagnostics Bringing high-throughput sequencing into clinical application Leonardo A. Meza-Zepeda, PhD Translational Genomics Group Institute for Cancer Research Leonardo.Meza-Zepeda@rr-research.no
P. Tang ( 鄧致剛 ); PJ Huang ( 黄栢榕 ) g( ); g ( ) Bioinformatics Center, Chang Gung University.
Databases and Tools for High Throughput Sequencing Analysis P. Tang ( 鄧致剛 ); PJ Huang ( 黄栢榕 ) g( ); g ( ) Bioinformatics Center, Chang Gung University. HTseq Platforms Applications on Biomedical Sciences
Mutation 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,
Next generation sequencing analysis - A UK perspective. Nicholas Lea
Next generation sequencing analysis - A UK perspective Nicholas Lea King s HMDC LMH is part of an integrated pathology service at King s Haematological Malignancy Diagnostic Centre (HMDC) HMDC serves population
Breast 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
SUPPLEMENTARY INFORMATION
doi: 1.138/nature8645 Physical coverage (x haploid genomes) 11 6.4 4.9 6.9 6.7 4.4 5.9 9.1 7.6 125 Neither end mapped One end mapped Chimaeras Correct Reads (million ns) 1 75 5 25 HCC1187 HCC1395 HCC1599
Not IN Our Genes - A Different Kind of Inheritance.! Christopher Phiel, Ph.D. University of Colorado Denver Mini-STEM School February 4, 2014
Not IN Our Genes - A Different Kind of Inheritance! Christopher Phiel, Ph.D. University of Colorado Denver Mini-STEM School February 4, 2014 Epigenetics in Mainstream Media Epigenetics *Current definition:
Genomic Medicine: What every pathologist needs to know
Genomic Medicine: What every pathologist needs to know Stephen P. Ethier, Ph.D. Professor, Department of Pathology and Laboratory Medicine, MUSC Director, MUSC Center for Genomic Medicine Genomics and
Introduction to Systems Biology of Cancer Lecture 2
Introduction to Systems Biology of Cancer Lecture 2 Gustavo Stolovitzky IBM Research Icahn School of Medicine at Mt Sinai DREAM Challenges High throughput measurements: The age of omics Systems Biology
Nature 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
Computational Analysis of UHT Sequences Histone modifications, CAGE, RNA-Seq
Computational Analysis of UHT Sequences Histone modifications, CAGE, RNA-Seq Philipp Bucher Wednesday January 21, 2009 SIB graduate school course EPFL, Lausanne ChIP-seq against histone variants: Biological
Introduction of an NGS gene panel into the Haemato-Oncology MPN service
Introduction of an NGS gene panel into the Haemato-Oncology MPN service Dr. Anna Skowronska, Dr Jane Bryon, Dr Samuel Clokie, Dr Yvonne Wallis and Professor Mike Griffiths West Midlands Regional Genetics
BWA alignment to reference transcriptome and genome. Convert transcriptome mappings back to genome space
Whole genome sequencing Whole exome sequencing BWA alignment to reference transcriptome and genome Convert transcriptome mappings back to genome space genomes Filter on MQ, distance, Cigar string Annotate
Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA
www.impactjournals.com/oncotarget/ Oncotarget, Supplementary Materials 2016 Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) DNA Supplementary Materials
Structural 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,
Future applications of full length virus genome sequencing
Future applications of full length virus genome sequencing Paul Kellam Virus Genomics Revisiting early HIV resistance ideas AIDS 1991 Nature 1993 Virus genome sequencing Population or single genome Whole
Computer 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
TP53 ABERRATIONS Methodical considerations
TP53 ABERRATIONS Methodical considerations Sarka Pavlova University Hospital and Masaryk University, Brno, Czech republic Belgrade March 16-17, 2018 TP53 gene in CLL: modes of inactivation mutation(s)
A. ILEA 1* A. M. VLADAREANU 2 E. NICULESCU-MIZIL 3
Bulletin of the Transilvania University of Braşov Series VI: Medical Sciences Vol. 9 (58) No. 1-2016 THE SIMULTANEOUS OCCURRENCE OF THE BCR-ABL TRANSLOCATION AND THE Jak2V617F MUTATION. DETECTION AND DYNAMICS
MEDICAL GENOMICS LABORATORY. Next-Gen Sequencing and Deletion/Duplication Analysis of NF1 Only (NF1-NG)
Next-Gen Sequencing and Deletion/Duplication Analysis of NF1 Only (NF1-NG) Ordering Information Acceptable specimen types: Fresh blood sample (3-6 ml EDTA; no time limitations associated with receipt)
Genomic 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
MicroRNA-29a Reveals Oncogenic Role on Myeloid Malignancies by Regulating DNMT3A
MicroRNA-29a Reveals Oncogenic Role on Myeloid Malignancies by Regulating DNMT3A Heba Alkhatabi, PhD Assistant Professor Department of Medical Laboratory Collage of Applied Medical science King Abdul Aziz
Nature Genetics: doi: /ng Supplementary Figure 1. Clinical timeline for the discovery WES cases.
Supplementary Figure 1 Clinical timeline for the discovery WES cases. This illustrates the timeline of the disease events during the clinical course of each patient s disease, further indicating the available
AVENIO ctdna Analysis Kits The complete NGS liquid biopsy solution EMPOWER YOUR LAB
Analysis Kits The complete NGS liquid biopsy solution EMPOWER YOUR LAB Analysis Kits Next-generation performance in liquid biopsies 2 Accelerating clinical research From liquid biopsy to next-generation
RNA-seq Introduction
RNA-seq Introduction DNA is the same in all cells but which RNAs that is present is different in all cells There is a wide variety of different functional RNAs Which RNAs (and sometimes then translated
Introduction. Introduction
Introduction We are leveraging genome sequencing data from The Cancer Genome Atlas (TCGA) to more accurately define mutated and stable genes and dysregulated metabolic pathways in solid tumors. These efforts
MRC-Holland MLPA. Description version 29;
SALSA MLPA KIT P003-B1 MLH1/MSH2 Lot 1209, 0109. As compared to the previous lots 0307 and 1006, one MLH1 probe (exon 19) and four MSH2 probes have been replaced. In addition, one extra MSH2 exon 1 probe,
An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage
An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage Aaron M Newman1,2,7, Scott V Bratman1,3,7, Jacqueline To3, Jacob F Wynne3, Neville C W Eclov3, Leslie A Modlin3,
Somatic cancer applications of NGS in in vitro Diagnostics.
Somatic cancer applications of NGS in in vitro Diagnostics. Nitin Udar PhD In Vitro Diagnsotics Division Illumina, Inc. 2013 Illumina, Inc. All rights reserved. Illumina, IlluminaDx, BaseSpace, BeadArray,
News Release. Title Integrated molecular profiling of juvenile myelomonocytic leukemia
News Release Title Integrated molecular profiling of juvenile myelomonocytic leukemia Key Points We identified ALK/ROS1 tyrosine kinase fusions (DCTN1-ALK, RANBP2-ALK, and TBL1XR1-ROS1) in patients with
Profiles of gene expression & diagnosis/prognosis of cancer. MCs in Advanced Genetics Ainoa Planas Riverola
Profiles of gene expression & diagnosis/prognosis of cancer MCs in Advanced Genetics Ainoa Planas Riverola Gene expression profiles Gene expression profiling Used in molecular biology, it measures the
FONS 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
An innovative multi-dimensional NGS approach to understanding the tumor microenvironment and evolution
An innovative multi-dimensional NGS approach to understanding the tumor microenvironment and evolution James H. Godsey, Ph.D. Vice President, Research & Development Clinical Sequencing Division (CSD) Life
Accel-Amplicon Panels
Accel-Amplicon Panels Amplicon sequencing has emerged as a reliable, cost-effective method for ultra-deep targeted sequencing. This highly adaptable approach is especially applicable for in-depth interrogation
Identifying Mutations Responsible for Rare Disorders Using New Technologies
Identifying Mutations Responsible for Rare Disorders Using New Technologies Jacek Majewski, Department of Human Genetics, McGill University, Montreal, QC Canada Mendelian Diseases Clear mode of inheritance
underlying metastasis and recurrence in HNSCC, we analyzed two groups of patients. The
Supplementary Figures Figure S1. Patient cohorts and study design. To define and interrogate the genetic alterations underlying metastasis and recurrence in HNSCC, we analyzed two groups of patients. The
Understanding The Genetics of Diamond Blackfan Anemia
Understanding The Genetics of Diamond Blackfan Anemia Jason Farrar, MD jefarrar@ About Me Assistant Professor of Pediatrics at University of Arkansas for Medical Sciences & Arkansas Children s Hospital
Supplementary Tables. Supplementary Figures
Supplementary Files for Zehir, Benayed et al. Mutational Landscape of Metastatic Cancer Revealed from Prospective Clinical Sequencing of 10,000 Patients Supplementary Tables Supplementary Table 1: Sample
Introduction to Cancer Bioinformatics and cancer biology. Anthony Gitter Cancer Bioinformatics (BMI 826/CS 838) January 20, 2015
Introduction to Cancer Bioinformatics and cancer biology Anthony Gitter Cancer Bioinformatics (BMI 826/CS 838) January 20, 2015 Why cancer bioinformatics? Devastating disease, no cure on the horizon Major
Supplemental Information For: The genetics of splicing in neuroblastoma
Supplemental Information For: The genetics of splicing in neuroblastoma Justin Chen, Christopher S. Hackett, Shile Zhang, Young K. Song, Robert J.A. Bell, Annette M. Molinaro, David A. Quigley, Allan Balmain,
High-throughput transcriptome sequencing
High-throughput transcriptome sequencing Erik Kristiansson (erik.kristiansson@zool.gu.se) Department of Zoology Department of Neuroscience and Physiology University of Gothenburg, Sweden Outline Genome
Breast cancer. Risk factors you cannot change include: Treatment Plan Selection. Inferring Transcriptional Module from Breast Cancer Profile Data
Breast cancer Inferring Transcriptional Module from Breast Cancer Profile Data Breast Cancer and Targeted Therapy Microarray Profile Data Inferring Transcriptional Module Methods CSC 177 Data Warehousing
Epigenetics. Jenny van Dongen Vrije Universiteit (VU) Amsterdam Boulder, Friday march 10, 2017
Epigenetics Jenny van Dongen Vrije Universiteit (VU) Amsterdam j.van.dongen@vu.nl Boulder, Friday march 10, 2017 Epigenetics Epigenetics= The study of molecular mechanisms that influence the activity of
Genomic Instability. Kent Nastiuk, PhD Dept. Cancer Genetics Roswell Park Cancer Institute. RPN-530 Oncology for Scientist-I October 18, 2016
Genomic Instability Kent Nastiuk, PhD Dept. Cancer Genetics Roswell Park Cancer Institute RPN-530 Oncology for Scientist-I October 18, 2016 Previous lecturers supplying slides/notes/inspiration Daniel
OncoPPi Portal A Cancer Protein Interaction Network to Inform Therapeutic Strategies
OncoPPi Portal A Cancer Protein Interaction Network to Inform Therapeutic Strategies 2017 Contents Datasets... 2 Protein-protein interaction dataset... 2 Set of known PPIs... 3 Domain-domain interactions...
Nature Medicine: doi: /nm.4439
Figure S1. Overview of the variant calling and verification process. This figure expands on Fig. 1c with details of verified variants identification in 547 additional validation samples. Somatic variants
RASA: Robust Alternative Splicing Analysis for Human Transcriptome Arrays
Supplementary Materials RASA: Robust Alternative Splicing Analysis for Human Transcriptome Arrays Junhee Seok 1*, Weihong Xu 2, Ronald W. Davis 2, Wenzhong Xiao 2,3* 1 School of Electrical Engineering,
Chromothripsis: A New Mechanism For Tumorigenesis? i Fellow s Conference Cheryl Carlson 6/10/2011
Chromothripsis: A New Mechanism For Tumorigenesis? i Fellow s Conference Cheryl Carlson 6/10/2011 Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development Cell 144,
Enterprise Interest Thermo Fisher Scientific / Employee
Enterprise Interest Thermo Fisher Scientific / Employee A next-generation sequencing assay to estimate tumor mutation load from FFPE research samples Fiona Hyland. Director of R&D, Bioinformatics Clinical
SALSA MLPA probemix P241-D2 MODY mix 1 Lot D As compared to version D1 (lot D1-0911), one reference probe has been replaced.
mix P241-D2 MODY mix 1 Lot D2-0413. As compared to version D1 (lot D1-0911), one reference has been replaced. Maturity-Onset Diabetes of the Young (MODY) is a distinct form of non insulin-dependent diabetes
University of Pittsburgh Annual Progress Report: 2008 Formula Grant
University of Pittsburgh Annual Progress Report: 2008 Formula Grant Reporting Period July 1, 2011 June 30, 2012 Research Project 1: Project Title and Purpose Small Molecule Inhibitors of HIV Nef Signaling
Mapping by recurrence and modelling the mutation rate
Mapping by recurrence and modelling the mutation rate Shamil Sunyaev Broad Institute of M.I.T. and Harvard Current knowledge is from Comparative genomics Experimental systems: yeast reporter assays Potential
Viral genome sequencing: applications to clinical management and public health. Professor Judy Breuer
Viral genome sequencing: applications to clinical management and public health Professor Judy Breuer Why do whole viral genome sequencing Genome sequencing allows detection of multigenic resistance in
Abstract. 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
DOES 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
Ambient temperature regulated flowering time
Ambient temperature regulated flowering time Applications of RNAseq RNA- seq course: The power of RNA-seq June 7 th, 2013; Richard Immink Overview Introduction: Biological research question/hypothesis
SALSA MLPA probemix P315-B1 EGFR
SALSA MLPA probemix P315-B1 EGFR Lot B1-0215 and B1-0112. As compared to the previous A1 version (lot 0208), two mutation-specific probes for the EGFR mutations L858R and T709M as well as one additional
Session 6: Integration of epigenetic data. Peter J Park Department of Biomedical Informatics Harvard Medical School July 18-19, 2016
Session 6: Integration of epigenetic data Peter J Park Department of Biomedical Informatics Harvard Medical School July 18-19, 2016 Utilizing complimentary datasets Frequent mutations in chromatin regulators
Host 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
The Human Major Histocompatibility Complex
The Human Major Histocompatibility Complex 1 Location and Organization of the HLA Complex on Chromosome 6 NEJM 343(10):702-9 2 Inheritance of the HLA Complex Haplotype Inheritance (Family Study) 3 Structure
REGULATED SPLICING AND THE UNSOLVED MYSTERY OF SPLICEOSOME MUTATIONS IN CANCER
REGULATED SPLICING AND THE UNSOLVED MYSTERY OF SPLICEOSOME MUTATIONS IN CANCER RNA Splicing Lecture 3, Biological Regulatory Mechanisms, H. Madhani Dept. of Biochemistry and Biophysics MAJOR MESSAGES Splice
BASIC PROCEDURES SAMPLING, MATERIAL, SANGER SEQUENCING
Technical aspects of TP53 mutation analysis: BASIC PROCEDURES SAMPLING, MATERIAL, SANGER SEQUENCING Sarka Pavlova University Hospital and Masaryk University, Brno, Czech republic TP53 gene in CLL: KEEP
Protein Domain-Centric Approach to Study Cancer Somatic Mutations from High-throughput Sequencing Studies
Protein Domain-Centric Approach to Study Cancer Somatic Mutations from High-throughput Sequencing Studies Dr. Maricel G. Kann Assistant Professor Dept of Biological Sciences UMBC 2 The term protein domain
CDH1 truncating alterations were detected in all six plasmacytoid-variant bladder tumors analyzed by whole-exome sequencing.
Supplementary Figure 1 CDH1 truncating alterations were detected in all six plasmacytoid-variant bladder tumors analyzed by whole-exome sequencing. Whole-exome sequencing of six plasmacytoid-variant bladder
Supplementary Appendix
Supplementary Appendix This appendix has been provided by the authors to give readers additional information about their work. Supplement to: Patel JP, Gönen M, Figueroa ME, et al. Prognostic relevance