Using the Bravo Liquid-Handling System for Next Generation Sequencing Sample Prep
|
|
- Joseph Armstrong
- 5 years ago
- Views:
Transcription
1 Using the Bravo Liquid-Handling System for Next Generation Sequencing Sample Prep Tom Walsh, PhD Division of Medical Genetics University of Washington
2 Next generation sequencing Sanger sequencing gold standard for over 30 years Next Generation Sequencing is massively parallel Millions of short reads, each bp 1,000-10,000 fold more sequence data Very low cost per base
3 Target enrichment Current sequence capacity enables whole genome sequencing (3000Mb) or whole exome coding regions (40Mb) Target enrichment allows specific capture and sequencing of only the genes associated with a particular disease/phenotype Smaller sequencing target = reduced cost/higher sample throughput Applying target enrichment and sequencing to the detection of mutations that predispose women to developing breast and ovarian cancer
4 BRCA1 and BRCA2 Inherited mutations in BRCA1 and BRCA2 predispose to high risks of developing breast and ovarian cancer Clinical recommendations for women with BRCA1 and BRCA2 mutations include increased surveillance and risk reducing surgical removal of the ovaries and fallopian tubes after child-bearing is complete Advent of PARP inhibitors, which preferentially kill BRCA1 and BRCA2 mutated cancers, has increased the clinical incentive to identify mutation carriers
5 Family 1. BRCA1 c.2800 AA Family 1. BRCA1: 2800 AA 6 2 Pr 79 Pr 77 Br 59 Br V N N N V N N N V N N N 91 V N Br 74 Br 32 Br 45 Br 36 Ov Pr 57 Ov 61 N N N N V N V N N N V N N N V N N N V N N N 82 N N 81 V N N N 80 N N 79 N N 78 N N Pa 66 V N N N Br 54 N N 74 V N N N Co 54 V N N N Br 29 V N 58 N N Br 28 V N N N Br 45 N N 39 V N Br 27 Br Br 39 Br Br 34 Br 49 Br 29, 39 V N V N V N N N V N V N V N V N N N V N V N V N Br 25 V N Br 27 V N Two hits: Inherited mutation + somatic loss of wildtype allele Somatic mutation generally chromosomal deletion
6 Family 16. BRCA2 c.1310 AAGA Family 16 BRCA del AAAG -> 456 stop Pa Br Pr Es 68 VN NN VN NN VN NN VN 63 NN Br Br 65 Br Br VN NN NN VN NN VN NN 68 Br VN VN NN NN VN VN Br 35 Br VN VN VN VN NN
7 NHGRI, Breast Cancer Information Core BRCA1 Large genes, each with >1000 different cancer-predisposing mutations BRCA2
8 Mutation spectrum also includes large deletions and duplications not detectable by PCR
9 Genetic testing of BRCA1 and BRCA2 In the U.S., testing is carried out almost exclusively by Myriad Protocol is based on PCR amplification of individual exons followed by Sanger sequencing on capillary instruments Large deletions and duplications are detected by a second test (BART added in 2007) which measures copy number at exons
10 Genetic testing of BRCA1 and BRCA2 In the U.S., testing is carried out almost exclusively by Myriad Protocol is based on PCR amplification of individual exons followed by Sanger sequencing on capillary instruments Large deletions and duplications are detected by a second test (BART added in 2007) which measures copy number at exons Our goal: develop a comprehensive next generation sequencing approach for research testing of all breast cancer susceptibility genes
11 1. Rare multi organ cancer syndromes Li-Fraumeni : sarcomas, leukemias, breast p53 Cowden: thyroid, endometrial, breast PTEN Diffuse gastric cancer: gastric and breast CDH1 Peutz-Jeughers : colon and breast STK11 Lynch: colon, endometrial, ovarian Mismatch Repair genes
12 2. Moderate risk breast cancer genes BRCA-Fanconi Anemia complex ATM p53 Mutations in 9 genes lead to 2-4 fold increased risk of developing breast cancer Ub FANCD2 BARD1 BRCA1 P BRIP1 P P CHEK2 Lower risk than BRCA1 and BRCA2 but still >25% lifetime risk PTEN 70 RAD51 BRCA2 NBS1 PALB2 RAD51C Clinically relevant level of risk MRE11 RAD50
13 Capturing 21 breast cancer genes Capture exons, introns, untranslated regions and 10kb up/downstream Total capture size = 939kb High risk Moderate risk Rare syndromes Lynch syndrome BRCA1 PALB2 p53 MLH1 BRCA2 CHEK2 CDH1 MSH2 BRIP1 PTEN PMS1 NBS1 STK11 PMS2 RAD50 MUTYH MRE11 ATM RAD50/51C
14 Capture design In solution capture with crna 120mer oligo baits (SureSelect) Repeat masked but allow 20bp overlap where exons are closely flanked by Alu repeats (BRCA1) crna baits (3x tiling) BRCA1 Repeat Tile through segmentally duplicated genes (CHEK2, PMS2, PTEN)
15 Developing a one stop genetic test Simultaneously capture and sequence 21 genes known to predispose to breast and/or ovarian cancer Detect all mutation classes Small: single base substitutions and indels Large: exon deletions and duplications Proof of principle: Test accuracy, sensitivity and specificity with 21 previously identified mutations from 10 genes
16 Capture and Sequencing Paired-end library (200bp) Hybridize to biotinylated capture bait oligos (21 gene regions) Purify with streptavidin beads Sonicate (3µg DNA) 2x76bp reads (9 days) Identify SNP and indels (MAQ and BWA) Compare to dbsnp, mutation databases Identify CNVs (depth of coverage)
17 Test series results - small mutations 15/15 small mutations from 10 different genes accurately identified Nonsense, splice site, missense and indels (1 to 19bp) Zero false positive calls of mutations in any gene or any sample
18 Test series results - small mutations 15/15 small mutations from 10 different genes accurately identified Nonsense, splice site, missense and indels (1 to 19bp) Zero false positive calls of mutations in any gene or any sample
19 Test series results - small mutations 15/15 small mutations from 10 different genes accurately identified Nonsense, splice site, missense and indels (1 to 19bp) Zero false positive calls of mutations in any gene or any sample
20 Mutation detection within duplicated regions Ratio of wildtype to mutation containing reads ~ 50/50 One exception: CHEK2 1100delC, approximately 15% mutant reads chr22:29,091, 857 segmental duplications Partial CHEK2 pseudogenes are located on chromosomes 15 and 16 4 extra copies of the target region reduces mutant to wildtype signal
21 Test series results - large mutations 6/6 large mutations in BRCA1 and BRCA2 were accurately identified by depth of coverage ratios normalized for bait coverage and GC content BRCA1 Deletion exons Ratio 0.52 Deletion exons Duplication exon Deletion exons
22 Summary of proof of principle study DNA capture and sequencing is accurate and sensitive for detecting inherited mutations of clinically important genes Simultaneously evaluates all known breast and ovarian cancer genes Detects single base substitutions, indels and CNVs Accurate mutation detection in non unique regions of the genome
23 Increasing throughput by barcoding samples Sequence coverage is very high (1000x) with one sample per lane Barcoding and pooling samples reduces sequencing costs Hybridize individual samples to SureSelect baits then add unique 6bp barcoded primer after capture by PCR amplification Sequence barcode, demultiplex samples, analyze samples individually
24 Increasing throughput by barcoding samples Sequence coverage is very high (1000x) with one sample per lane Barcoding and pooling samples reduces sequencing costs Hybridize individual samples to SureSelect baits then add unique 6bp barcoded primer after capture by PCR amplification Sequence barcode, demultiplex samples, analyze samples individually Current throughput: 12 samples per lane, 96 per flow cell (GAIIx)
25 Multiplexing 96 barcoded samples per flow cell Median coverage is 350x 97% of targeted bases >100x minimum coverage
26 Data from multiplexing 96 barcoded samples Barcode Gene Mutation Within pool of 12 samples per lane Location (hg19) Wildtype Variant TGACCA BRCA1 4510del3insTT chr17:41,228,596-41,228, CAGATC BRCA1 5382insC chr17:41,228,596-41,228, TGACCA BRCA2 9179G>C chr13:32,953,650-32,953, GGCTAC BARD1 1210del21 chr2:215,645, ,645, CGATGT ATM 1027delGAAA chr2:215,645, ,645,
27 Data from multiplexing 96 barcoded samples Barcode Gene Mutation Within pool of 12 samples per lane Location (hg19) Wildtype Variant TGACCA BRCA1 4510del3insTT chr17:41,228,596-41,228, CAGATC BRCA1 5382insC chr17:41,228,596-41,228, TGACCA BRCA2 9179G>C chr13:32,953,650-32,953, GGCTAC BARD1 1210del21 chr2:215,645, ,645, CGATGT ATM 1027delGAAA chr2:215,645, ,645, BRCA2
28 Data from multiplexing 96 barcoded samples Barcode Gene Mutation Within pool of 12 samples per lane Location (hg19) Wildtype Variant TGACCA BRCA1 4510del3insTT chr17:41,228,596-41,228, CAGATC BRCA1 5382insC chr17:41,228,596-41,228, TGACCA BRCA2 9179G>C chr13:32,953,650-32,953, GGCTAC BARD1 1210del21 chr2:215,645, ,645, CGATGT ATM 1027delGAAA chr2:215,645, ,645, BRCA2 100x coverage enables accurate detection of all mutation classes
29 Library prep is now the bottleneck Prep time for 96 sequence ready libraries is 3 weeks with 3 FTEs Most labor intensive part is magnetic bead (SPRI) clean ups Pre capture library prep (SPRI clean up x5) Capture hybridization x1 Post captures washes and amplification (SPRI clean up x2)
30 Increasing throughput by automation x96 x1 Individual sample handling
31 Increasing throughput by automation x96 Individual sample handling x1 96 sample handling
32 Increasing throughput by automation All liquid handling, enzymatic incubations and post capture washes are performed on the deck x96 96 well magnet allows plate based SPRI clean up x1
33 Increasing throughput by automation Protocols can be edited easily and elution volumes changed x96 x1 Incorporated and validated post capture off bead PCR amplification
34 Summary Sample throughput increased with barcoding and automation With standalone Bravo: 96 samples sequence ready library preps no longer bottleneck Reduced from 3 weeks with 3 FTEs to 3 days with 1 FTE Manual tip box replacement (not so bad) Complete walk away automated system (on wish list)
35 Ongoing projects Ovarian cancer sequenced 21 genes in 384 patients All libraries prepped on Bravo, sequenced on 4 flowcells (GAIIx) Breast cancer 1900 high risk families (KingLab collection) Running 96 samples in single lane of a HiSeq 96 post capture barcodes (early access from Agilent R+D) Testing Bravo for exome capture with NimbleGen EZ cap oligos
36 Acknowledgments Ming Lee, PhD Bioinformatics pipeline Alex Nord CNV and breakpoint algorithms Anne Thornton, Chris Pennil, Silvia Casadei, PhD library prep Mary-Claire King, PhD and Elizabeth Swisher, MD National Cancer Institute, Dept of Defense, Komen for the Cure
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.
More informationGYNplus: A Genetic Test for Hereditary Ovarian and/or Uterine Cancer
GYNplus: A Genetic Test for Hereditary Ovarian and/or Uterine Cancer Causes of Hereditary Ovarian and Uterine Cancer uterine cancer ovarian cancer Sporadic 75-90% Sporadic 70-80% Hereditary, 5% Lynch syndrome
More informationAdvanced Ovarian Carcinoma
Advanced Ovarian Carcinoma What is our standard of care? IV carbo/taxol IP platinum/taxane (what regimen?) IV carbo/taxol/bevacizumab + 12 months of Bev IV carbo + dose dense taxol Controversy between
More informationNGS for Cancer Predisposition
NGS for Cancer Predisposition Colin Pritchard MD, PhD University of Washington Dept. of Lab Medicine AMP Companion Society Meeting USCAP Boston March 22, 2015 Disclosures I am an employee of the University
More informationMultiplex 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
More informationGermline Testing for Hereditary Cancer with Multigene Panel
Germline Testing for Hereditary Cancer with Multigene Panel Po-Han Lin, MD Department of Medical Genetics National Taiwan University Hospital 2017-04-20 Disclosure No relevant financial relationships with
More information6/8/17. Genetics 101. Professor, College of Medicine. President & Chief Medical Officer. Hereditary Breast and Ovarian Cancer 2017
Genetics 101 Hereditary Breast and Ovarian Cancer 2017 Rebecca Sutphen, MD, FACMG Professor, College of Medicine President & Chief Medical Officer INVASIVE CANCER GENETICALLY ALTERED CELL HYPERPLASIA DYSPLASIA
More informationGYNplus. genetic testing for hereditary ovarian and/or uterine cancer
GYNplus genetic testing for hereditary ovarian and/or uterine cancer What Are the Causes of Hereditary Ovarian and Uterine Cancer? uterine cancer ovarian cancer sporadic 70-80% hereditary 5% Lynch syndrome
More informationThe Genetics of Breast and Ovarian Cancer Prof. Piri L. Welcsh
The Genetics of Breast Piri L. Welcsh, PhD Research Assistant Professor University of Washington School of Medicine Division of Medical Genetics 1 Genetics of cancer All cancers arise from genetic and
More informationHereditary Breast and Ovarian Cancer Rebecca Sutphen, MD, FACMG
Hereditary Breast and Ovarian Cancer 2015 Rebecca Sutphen, MD, FACMG Among a consecutive series of 11,159 women requesting BRCA testing over one year, 3874 responded to a mailed survey. Most respondents
More informationBRCAplus. genetic testing for hereditary breast cancer
BRCAplus genetic testing for hereditary breast cancer Developed in collaboration with Fox Chase Cancer Center and the Arcadia University Genetic Counseling Program. Causes of Hereditary Breast Cancer familial
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 informationMSI positive MSI negative
Pritchard et al. 2014 Supplementary Figure 1 MSI positive MSI negative Hypermutated Median: 673 Average: 659.2 Non-Hypermutated Median: 37.5 Average: 43.6 Supplementary Figure 1: Somatic Mutation Burden
More informationCentoCancer STRIVE FOR THE MOST COMPLETE INFORMATION
CentoCancer STRIVE FOR THE MOST COMPLETE INFORMATION CentoCancer our most comprehensive oncogenetics panel for hereditary mutations Hereditary pathogenic variants confer an increased risk of developing
More informationThe Next Generation of Hereditary Cancer Testing
The Next Generation of Hereditary Cancer Testing Why Genetic Testing? Cancers can appear to run in families. Often this is due to shared environmental or lifestyle patterns, such as tobacco use. However,
More informationWHAT IS A GENE? CHROMOSOME DNA PROTEIN. A gene is made up of DNA. It carries instructions to make proteins.
WHAT IS A GENE? CHROMOSOME E GEN DNA A gene is made up of DNA. It carries instructions to make proteins. The proteins have specific jobs that help your body work normally. PROTEIN 1 WHAT HAPPENS WHEN THERE
More informationTumorNext-HRD with OvaNext: Paired Germline and Tumor Analyses of Genes Involved in
SAMPLE REPORT Ordered By Contact ID:1251298 Example, Doctor, MD MOCKORG44 (10829) 123 Somewhere LaneSuite 4 Heaven NV 78872 US Ph:123-123-1234 Fx:123-123-1223 Org ID:8141 Normal Specimen Accession #: 00-086947
More informationWHAT IS A GENE? CHROMOSOME DNA PROTEIN. A gene is made up of DNA. It carries instructions to make proteins.
WHAT IS A GENE? CHROMOSOME GENE DNA A gene is made up of DNA. It carries instructions to make proteins. The proteins have specific jobs that help your body work normally. PROTEIN 1 WHAT HAPPENS WHEN THERE
More informationMultigene Panel Testing for Hereditary Cancer Risk
Multigene Panel Testing for Hereditary Cancer Risk Dana Zakalik, M.D. Director, Nancy and James Grosfeld Cancer Genetics Center Professor, OUWB Medical School MCC Annual Meeting November 4, 2015 Outline
More informationGEN ETICS AN D GEN OM ICS IN CANCER PREVENTION AN D TREATM EN T. Robert Nathan Slotnick MD PhD Director, Medical Genetics and Genomics
GEN ETICS AN D GEN OM ICS IN CANCER PREVENTION AN D TREATM EN T Robert Nathan Slotnick MD PhD Director, Medical Genetics and Genomics The Medical/Surgical/Radiation Oncologist s View of Genetics Cancer
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 informationGenetic Testing for BRCA1 and BRCA2 Genes
Genetic Testing for BRCA1 and BRCA2 Genes MP9478 Covered Service: Prior Authorization Required: Additional Information: Yes when meets criteria below Yes as shown below Pre and post-test genetic counseling
More informationMEDICAL POLICY Genetic Testing for Breast and Ovarian Cancers
POLICY: PG0067 ORIGINAL EFFECTIVE: 07/30/02 LAST REVIEW: 01/25/18 MEDICAL POLICY Genetic Testing for Breast and Ovarian Cancers GUIDELINES This policy does not certify benefits or authorization of benefits,
More informationThe Value of Panel Testing in Inherited Breast Cancer Risk Assessment. Rodney J. Scott Division of Molecular Medicine
The Value of Panel Testing in Inherited Breast Cancer Risk Assessment Rodney J. Scott Division of Molecular Medicine Mutation Detection Next Generation DNA sequencing has revolutionised mutation detection
More informationUW359 Ovary 3c 3 Serous Recurrent 68 BRCA1 816delGT BRCA1 del exon 1-2. UW417 Ovary 3c 3 Serous Primary 38 BRCA1 1675delA
Supplementary Table 1. Cases with deleterious germline mutations, somatic HR mutations, and somatic PTEN mutations. ID Site Stage Grade Histology Tumor Age Germline mutation(s) a Somatic HR mutation(s)
More informationInvestigating rare diseases with Agilent NGS solutions
Investigating rare diseases with Agilent NGS solutions Chitra Kotwaliwale, Ph.D. 1 Rare diseases affect 350 million people worldwide 7,000 rare diseases 80% are genetic 60 million affected in the US, Europe
More informationAssessment and Management of Genetic Predisposition to Breast Cancer. Dr Munaza Ahmed Consultant Clinical Geneticist 2/7/18
Assessment and Management of Genetic Predisposition to Breast Cancer Dr Munaza Ahmed Consultant Clinical Geneticist 2/7/18 Overview The role of the Cancer Genetics team NICE guidelines for Familial Breast
More informationPredictive and Diagnostic Testing for Cancer in Women. Aparna Rajadhyaksha MD
Predictive and Diagnostic Testing for Cancer in Women Aparna Rajadhyaksha MD Hereditary Cancer s in Women BRCA1 &2 Other Breast Cancer Genes Li Fraumeni PTEN CHEK2 BRCA1&2 t BRCA1 is part of a complex
More informationLearn your genetic risk for the most common hereditary cancers.
Learn your genetic risk for the most common hereditary cancers. color.com Color analyzes 30 genes including BRCA1 and BRCA2 to help women and men understand their risk for the most common hereditary cancers,
More informationRicombinazione omologa nel carcinoma ovarico: BRCA e oltre. F. Raspagliesi MD
Ricombinazione omologa nel carcinoma ovarico: BRCA e oltre F. Raspagliesi MD raspagliesi@istitutotumori.mi.it BRCA molecular signature in ovarian cancer In a pooled analysis of 26 observational studies
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 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 informationGenetic Testing for BRCA1 and BRCA2 Genes
Genetic Testing f BRCA1 and BRCA2 Genes MP9478 Covered Service: Pri Authization Required: Additional Infmation: Yes when meets criteria below Yes--as shown below Pre and post-test genetic counseling is
More informationPREPARED FOR: U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland
AWARD NUMBER: W81XWH-13-1-0421 TITLE: The Fanconi Anemia BRCA Pathway as a Predictor of Benefit from Bevacizumab in a Large Phase III Clinical Trial in Ovarian Cancer PRINCIPAL INVESTIGATOR: Elizabeth
More informationEnabling Personalized
Molecular Enabling Personalized Diagnostics Medicine- Targeted Sequencing: NGS-based solutions Silvia Dorn Roel Reinders- Andreas Diplas Friday, 19.06.2015 Company Overview Founded in April 2011 Development
More informationMEDICAL 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)
More informationCancer Risks Associated With Inherited Mutations in Ovarian Cancer Susceptibility Genes Beyond BRCA1 and BRCA2
AWARD NUMBER: W81XWH-15-1-0084 TITLE: Cancer Risks Associated With Inherited Mutations in Ovarian Cancer Susceptibility Genes Beyond BRCA1 and BRCA2 PRINCIPAL INVESTIGATOR: Elizabeth Swisher CONTRACTING
More informationHereditary Cancer Update Strengthening Linkages Workshop April 22, 2017
Hereditary Cancer Update Strengthening Linkages Workshop April 22, 2017 Renée Perrier, MD MSc FRCPC Clinical Assistant Professor University of Calgary, Department of Medical Genetics Medical Director,
More informationA pathogenic mutation was identified in the BRCA1 gene.
Hereditary Cancer Risk Test ORDERING PHYSICIAN Dr. Jenny Jones Sample Medical Group 123 Main St. Sample, CA SPECIMEN Type: Saliva Barcode: 223 234234 2343 Collected: Apr 13, 2016 Received: Apr 14, 2016
More informationIdentifying 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
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 informationBWA 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
More informationGenetic Risk Assessment for Cancer
Genetic Risk Assessment for Cancer Jennifer Siettmann, MS CGC Certified Genetic Counselor/Cancer Risk Counselor Banner Good Samaritan Cancer Screening & Prevention Program Objectives Describe the role
More informationAre you at risk of Hereditary Cancer? Your Guide to the Answers
Are you at risk of Hereditary Cancer? Your Guide to the Answers What is Hereditary Cancer? The genes we are born with may contribute to our risk of developing certain types of cancer, including breast,
More informationCorporate Medical Policy
Corporate Medical Policy Moderate Penetrance Variants Associated with Breast Cancer in File Name: Origination: Last CAP Review: Next CAP Review: Last Review: moderate_penetrance_variants_associated_with_breast_cancer_
More informationGenetic Determinants, Risk Assessment and Management
Genetic Determinants, Risk Assessment and Management Rachel Rando, MS, CGC Genetic Counselor Hunterdon Regional Cancer Center Flemington, NJ I have no disclosures. Acknowledgements: Staff of Hunterdon
More informationA Patient s Guide to Hereditary Cancer. Is Hereditary Cancer Testing Right for You?
A Patient s Guide to Hereditary Cancer Is Hereditary Cancer Testing Right for You? What is Hereditary Cancer? Most cancers occur in people who do not have a strong family history of that cancer. This is
More informationNo mutations were identified.
Hereditary High Cholesterol Test ORDERING PHYSICIAN PRIMARY CONTACT SPECIMEN Report date: Aug 1, 2017 Dr. Jenny Jones Sample Medical Group 123 Main St. Sample, CA Kelly Peters Sample Medical Group 123
More informationFamily Assessment. Objectives. Comprehensive Family History Important Inexpensive Underutilized genetic tool
Besides the BRCA genes, what else to consider in hereditary breast and ovarian cancer? Laurie M. Connors DNP, APNG, FNP-BC, AGN-BC Objectives Evaluate personal & family history to assess risk for hereditary
More informationAVENIO 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
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 informationBe Ready Pack Learn more about how Myriad myrisk is revolutionizing hereditary cancer testing.
Be Ready Pack Learn more about how Myriad myrisk is revolutionizing hereditary cancer testing. Hereditary cancer and you Approximately 5% to 10% of all cancers develop because a person inherited a genetic
More informationGenetic Panel Testing and Implications for Cancer Care
Genetic Panel Testing and Implications for Cancer Care Dana Zakalik, M.D. Nancy and James Grosfeld Cancer Genetics Center Professor, OUWB Medical School MCC Board of Directors Meeting September 28, 2016
More informationA guide to genetic testing for hereditary cancers
Cancer Testing Solutions A guide to genetic testing for hereditary cancers The benefit of knowing TM Hereditary cancer genetic testing can play a critical role in managing health Cancer touches millions
More informationSchedule of Accreditation issued by United Kingdom Accreditation Service 2 Pine Trees, Chertsey Lane, Staines-upon-Thames, TW18 3HR, UK
2 Pine Trees, Chertsey Lane, Staines-upon-Thames, TW18 3HR, UK NW Thames Regional Genetics Laboratory Northwick Park Hospital Watford Road Harrow HA1 3UJ United Kingdom Contact: Caroline Sullivan Tel:
More informationMultiple gene sequencing for risk assessment in patients with early-onset or familial breast cancer
www.impactjournals.com/oncotarget/ Oncotarget, Supplementary Materials 2016 Multiple gene sequencing for risk assessment in patients with early-onset or familial breast cancer Supplementary Materials Supplementary
More informationCASE STUDY. Germline Cancer Testing in A Proband: Extension of Benefits to Unaffected Family Members. Introduction. Patient Profile.
CASE STUDY Germline Cancer Testing in A Proband: Extension of Benefits to Unaffected Family Members Introduction Most cancers are caused by genetic damage resulting from random mutations and exposure to
More informationThe benefit of. knowing. Genetic testing for hereditary cancer. A patient support guide
The benefit of knowing Genetic testing for hereditary cancer A patient support guide Does cancer run in your family? Cancer is more common in some families. Sometimes cancer is caused by a change in a
More informationCarol Christianson, MS, CGC Genetic Counselor West Michigan Cancer Center
Carol Christianson, MS, CGC Genetic Counselor West Michigan Cancer Center Following this presentation you will be able to: Identify cancer survivors in your practice who might benefit from genetic counseling
More informationUse of panel tests in place of single gene tests in the cancer genetics clinic
Clin Genet 2015: 88: 278 282 Printed in Singapore. All rights reserved CLINICAL GENETICS doi: 10.1111/cge.12488 Short Report se of panel tests in place of single gene tests in the cancer genetics clinic
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 informationAccel-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
More informationGenetic testing and pancreatic disease
Genetic testing and pancreatic disease February 2 d, 2018 Yale Pancreas Symposium 2018: Multidisciplinary Management of Pancreatic Cancer Xavier Llor, M.D., PhD. Associate Professor of Medicine Co-Director,
More informationObjectives. Genetics in Cancer Treatment and Prevention. Genes
Objectives Genetics in Cancer Treatment and Prevention Cheryl LaFlore, ARNP, MSN, BC Understand how to integrate genetic and genomic information into oncology nursing practice Define the role of an oncology
More informationCharacterisation 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
More informationGenetic Testing Today: What Genes Can Tell Us. Living Beyond Breast Cancer Conference Kara N. Maxwell, MD, PhD University of Pennsylvania
Genetic Testing Today: What Genes Can Tell Us Living Beyond Breast Cancer Conference Kara N. Maxwell, MD, PhD University of Pennsylvania Overview of talk PART 1: Overview of Genetics PART 2: BRCA1/2 PART
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 informationCytogenetics 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
More informationThe Role of Genetics in Ovarian Cancer Screening. Dawn DeLozier, Ph.D. Medical Geneticist, SAMC Associate Professor UCSF-Fresno
The Role of Genetics in Ovarian Cancer Screening Dawn DeLozier, Ph.D. Medical Geneticist, SAMC Associate Professor UCSF-Fresno How Much Breast and Ovarian Cancer Is Hereditary? 15%-20% 5%-10% Breast Cancer
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 informationOvaNext. patient guide. genetic testing for hereditary breast, ovarian, and uterine cancer
patient guide OvaNext genetic testing for hereditary breast, ovarian, and uterine cancer Because knowing your risk can mean early detection and prevention About half of the women diagnosed with uterine
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 informationGermline Genetic Testing for Breast Cancer Risk
Kathmandu, Bir Hospital visit, August 2018 Germline Genetic Testing for Breast Cancer Risk Evidence-based Genetic Screening Rodney J. Scott Demography in New South Wales (total population ~ 7,000,000)
More information10/21/ New Release, Quest Diagnostics Nichols Institute, Valencia
NEW TESTS Please Note: Not all test codes assigned to each assay are listed in the table of contents. Please refer to the complete listing on the page numbers indicated. Test Code Test Name Effective Date
More informationMEDICAL GENOMICS LABORATORY. Peripheral Nerve Sheath Tumor Panel by Next-Gen Sequencing (PNT-NG)
Peripheral Nerve Sheath Tumor Panel by Next-Gen Sequencing (PNT-NG) Ordering Information Acceptable specimen types: Blood (3-6ml EDTA; no time limitations associated with receipt) Saliva (OGR-575 DNA Genotek;
More informationAVENIO 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
More informationGenetic Risk Assessment for Cancer
Genetic Risk Assessment for Cancer Jennifer Siettmann, MS CGC Certified Genetic Counselor Banner MD Anderson Cancer Center Objectives Describe the role of genetic counseling and genetic testing in patient
More informationWhy Test for Hereditary Cancer in Preventive Care?
Why Test for Hereditary Cancer in Preventive Care? Millions of people are sidelined by cancer. Wouldn't it be worth it for your patients to know their risk? background HEREDITARY (5-10%) More than 1 in
More informationHereditary Cancer Risk Assessment for Gynecological Cancers. FarrNezhatMD.com
Hereditary Cancer Risk Assessment for Gynecological Cancers FarrNezhatMD.com Image credit: PLOS blogs 5-10% hereditary 10-20% 70-80% sporadic Genetic Changes and Cancer Cancer begins with a genetic
More informationNGS 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
More informationMyriad Financial Assistance Program (MFAP)
Myriad Financial Assistance Program (MFAP) MEDICAL CRITERIA Hereditary Cancer Products The Myriad Financial Assistance Program offers aid to patients who meet specific financial and medical requirements.
More informationSupplementary 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
More information11/29/2017. Genetics and Cancer ERICA L SILVER, MS, LCGC GENETIC COUNSELOR. Genetics 101. Transcription vs Translation
Genetics and Cancer ERICA L SILVER, MS, LCGC GENETIC COUNSELOR Genetics 101 Transcription vs Translation 1 Carcinogenesis and Genetics Normal cell First mutation First mutation Second mutation Second mutation
More informationIlluminating the genetics of complex human diseases
Illuminating the genetics of complex human diseases Michael Schatz Sept 27, 2012 Beyond the Genome @mike_schatz / #BTG2012 Outline 1. De novo mutations in human diseases 1. Autism Spectrum Disorder 2.
More informationTITLE: - Whole Genome Sequencing of High-Risk Families to Identify New Mutational Mechanisms of Breast Cancer Predisposition
AD Award Number: W81XWH-13-1-0336 TITLE: - Whole Genome Sequencing of High-Risk Families to Identify New Mutational Mechanisms of Breast Cancer Predisposition PRINCIPAL INVESTIGATOR: Mary-Claire King,
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 informationHereditary Cancer Products
Hereditary Products Integrated BRACAnalysis (BRCA1 and BRCA2 sequencing and large rearrangement testing (BART)), covered when: PERSONAL HISTORY of Breast (must meet at least 1) Diagnosed
More informationIdentification of genomic alterations in cervical cancer biopsies by exome sequencing
Chapter- 4 Identification of genomic alterations in cervical cancer biopsies by exome sequencing 105 4.1 INTRODUCTION Athough HPV has been identified as the prime etiological factor for cervical cancer,
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 informationCANCER GENETICS PROVIDER SURVEY
Dear Participant, Previously you agreed to participate in an evaluation of an education program we developed for primary care providers on the topic of cancer genetics. This is an IRB-approved, CDCfunded
More informationGermline Mutations in CHEK1 and CHEK2 in Women with Ovarian, Peritoneal, or Fallopian Tube Cancer
Walden University ScholarWorks Walden Dissertations and Doctoral Studies Walden Dissertations and Doctoral Studies Collection 2015 Germline Mutations in CHEK1 and CHEK2 in Women with Ovarian, Peritoneal,
More informationInformation for You and Your Family
Information for You and Your Family What is Prevention? Cancer prevention is action taken to lower the chance of getting cancer. In 2017, more than 1.6 million people will be diagnosed with cancer in the
More informationManagement of BRCA Positive Breast Cancer. Archana Ganaraj, MD February 17, 2018 UPDATE ON WOMEN S HEALTH
Management of BRCA Positive Breast Cancer Archana Ganaraj, MD February 17, 2018 UPDATE ON WOMEN S HEALTH The number of American women who have lost their lives to breast cancer outstrips the total number
More informationEvaluation of BRCA1/2 and homologous recombination defects in ovarian cancer and impact on clinical outcomes
Evaluation of BRCA1/2 and homologous recombination defects in ovarian cancer and impact on clinical outcomes Melinda S. Yates, PhD Department of Gynecologic Oncology & Reproductive Medicine University
More informationGenetic Testing For Ovarian Cancer: When, How And Who? Judith Balmaña, MD, PhD University Hospital Vall d Hebron Barcelona, Spain
Genetic Testing For Ovarian Cancer: When, How And Who? Judith Balmaña, MD, PhD University Hospital Vall d Hebron Barcelona, Spain Why Would We Consider Genetic Testing in Patients With Ovarian Cancer?
More informationpatient guide CancerNext genetic testing for hereditary cancer Because knowing your risk can mean early detection and prevention
patient guide CancerNext genetic testing for hereditary cancer Because knowing your risk can mean early detection and prevention Know the Basics Cancer occurs in about 1 in 3 adults in their lifetime types
More informationCOLON CANCER & GENETICS VERMONT COLORECTAL CANCER SUMMIT NOVEMBER 15, 2014
COLON CANCER & GENETICS VERMONT COLORECTAL CANCER SUMMIT NOVEMBER 15, 2014 WENDY MCKINNON, MS, CGC CERTIFIED GENETIC COUNSELOR FAMILIAL CANCER PROGRAM UNIVERSIT Y OF VERMONT MEDICAL CENTER 1 CHARACTERISTICS
More informationHereditary Breast and Ovarian Cancer Screening & Genetic Counseling
Hereditary Breast and Ovarian Cancer Screening & Genetic Counseling Cecelia Bellcross, PhD, MS, CGC Emory University School of Medicine Department of Human Genetics The First Line of Defense February 21,
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 information