A dedication to sharing

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We believe there’s a new gold standard today, one that includes both high quality testing and a dedication to improving medicine.

Peer reviewed papers

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Posters & presentations

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Scientific publications

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.
Genetics in Medicine. Published online May 11, 2017. doi:10.1038/gim.2017.37
Consistency of BRCA1 and BRCA2 variant classifications among clinical diagnostic laboratories.
Lincoln SE, Yang S, Cline MS, Kobayashi Y, Zhang C, Topper S, Haussler D, Paten B, Nussbaum RL.
JCO Precision Oncology. Published online April 11, 2017. doi:10.1200/PO.16.00020
Pathogenic variant burden in the ExAC database: An empirical approach to evaluating population data for clinical variant interpretation.
Kobayashi Y, Yang S, Nykamp K, Garcia J, Lincoln SE, Topper SE.
Genome Medicine. 20179, 13. doi:10.1186/S13073-017-0403-7
Clinical genetics testing laboratories have a remarkably low rate of clinically significant discordance when interpreting variants in hereditary cancer syndrome genes.
Nussbaum RL, Yang S, Lincoln SE.
Journal of Clinical Oncology. Published online January 30, 2017. doi:10.1200/JCO.2016.70.9451
Data sharing and reproducible clinical genetic data: Success and challenges.
Yang S, Cline M, Zhang C, Paten B, Lincoln SE.
Pacific Symposium on Biocomput. 201622, 166-176. doi:10.1142/9789813207813_0017
Clinical genetic testing for the cardiomyopathies and arrhythmias: A systematic framework for establishing clinical validity and addressing genotypic and phenotypic heterogeneity.
Garcia J, Tahiliani J, Johnson NM, Aguilar S, Beltran D, Daly A, Decker E, Haverfield E, Herrera B, Murillo L, Nykamp K, Topper S.
Frontiers in Cardiovascular Medicine. 2016, 3(20). doi:10.3389/fcvm.2016.00020
Germline hemizygous deletion of CDKN2A–CDKN2B locus in a patient presenting with Li–Fraumeni syndrome.
Chan SH, Lim WK, Michalski ST, Lim JQ, Binte Ishak ND, Met-Domestici M, Chuan Young CN, Vikstrom K, Esplin ED, Fulbright J, Ang MK, Wee J, Sittampalam K, Farid M, Lincoln SE, Itahana K, Abdullah S, Teh BT, Ngeow J.
NPJ Genomic Medicine. 2016, 1, 16015. doi:10.1038/npjgenmed.2016.15
Who pays? Coverage challenges for cardiovascular genetic testing in U.S. patients.
Spoonamore K, Johnson NM.
Frontiers in Cardiovascular Medicine. 2016, 3(14). doi:10.3389/fcvm.2016.00014
Comprehensive versus targeted genetic testing in children with hypertrophic cardiomyopathy.
Bales ND, Johnson NM, Judge DP, Murphy AM.
Pediatric Cardiology. 2016, 37(5), 845. doi:10.1007/s00246-016-1358-y
An individual with both MUTYH-associated polyposis and Lynch syndrome identified by multi-gene hereditary cancer panel testing: A case report.
Cohen SA, Tan CA, Bisson R.
Frontiers in Genetics. 20167, 1. doi:10.3389/fgene.2016.00036
Autosomal recessive MFN2-related Charcot-Marie-Tooth disease with diaphragmatic weakness: Case report and literature review.
Tan CA, Rabideau M, Blevins A, Westbrook MJ, Ekstein T, Nykamp K, Deucher A, Harper A, Demmer L.
American Journal of Medical Genetics Part A. 2016, 170(6), 1552-4833. doi:10.1002/ajmg.a.37611
Genetic counselors in startup companies: Redefining the genetic counselor role.
Rabideau MM, Wong K, Gordon ES, Ryan L.
Journal of Genetic Counselling. 2016, 25(4), 649–657. doi:10.1007/s10897-015-9923-8
Clinical actionability of multigene panel testing for hereditary breast and ovarian cancer risk assessment.
Desmond A, Kurian AW, Gabree M, Mills MA, Anderson MJ, Kobayashi Y, Horick N, Yang S, Shannon KM, Tung N, Ford JM, Lincoln SE, Ellisen LW.
JAMA Oncology. 2015, 1(7), 943-951. doi:10.1001/jamaoncol.2015.2690
A systematic comparison of traditional and multigene panel testing for hereditary breast and ovarian cancer genes in more than 1000 patients.
Lincoln S, Kobayashi Y, Anderson M, Yang S, Desmond AJ, Mills MA, Nilsen GB, Jacobs KB, Monzon FA, Kurian AW, Ford JM, Ellisen LW.
The Journal of Molecular Diagnostics. 2015, 17(5), 533-544. doi:10.1016/j.jmoldx.2015.04.009
Low-level constitutional mosaicism of a de novoBRCA1 gene mutation.
Friedman E, Efrat N, Soussan-Gutman L, Dvir A, Kaplan Y, Ekstein T, Nykamp K, Powers M, Rabideau M, Sorenson J, Topper S.
British Journal of Cancer. 2015, 112, 765–768. doi:10.1038/bjc.2015.14
A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.
Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.
Bioinformatics. 2015, 31(2), 268-270. doi:10.1093/bioinformatics/btu630
Clinical evaluation of a multiple-gene sequencing panel for hereditary cancer risk assessment.
Kurian AW, Hare EE, Mills MA, Kingham KE, McPherson L, Whittemore AS, McGuire V, Ladabaum U, Kobayashi Y, Lincoln SE, Cargill M, Ford JM.
Journal of Clinical Oncology. 2014, 32(19), 2001-2009. doi:10.1200/JCO.2013.53.6607

2017 Posters and Presentations

American Society of Clinical Oncology (ASCO) Annual Meeting

June 2-6, 2017
Chicago, IL

POSTERS

Determining the clinical value of germline genetic testing coupled with tumor mutation profiling

Need for re-evaluation of current guidelines based on results from germline genetic testing in prostate cancer

Unexpected germline mutations in a pan-cancer analysis including sarcoma, renal, and other cancers

Heart Rhythm Society (HRS) Scientific Sessions

May 10-13, 2017
Chicago, IL

PRESENTATION

Pathogenic variants in calmodulin associated with resuscitated childhood cardiac arrest

American Society of Breast Surgeons (ASBS)

April 26-30, 2017
Las Vegas, NV

POSTERS

Expanded gene panel utilization in women with breast cancer: identification and intervention beyond breast cancer risk

Hereditary cancer risk: A growing body of evidence supporting broader testing

Breast surgeon consultation with remote genetic counselor improves clinical decision-making

ACMG Annual Clinical Genetics Meeting

March 21-25, 2017
Phoenix, AZ

POSTERS

Attitudes of healthy early adopters toward professional genome sequencing: Observations from the PeopleSeq Consortium

The benefit of a medically actionable genetic screening panel in healthy individuals: A case report

Canavan disease research: Forming a Patient Insights Network for the Canavan disease community

CNV analysis of ACADM enhances yield in the molecular diagnosis of medium-chain acyl-CoA dehydrogenase deficiency

Contiguous 2p16.3p21 gene deletion including EPCAM, MSH2, and MSH6 identified with next-generation sequencing

Co-occurrence of pathogenic variants in MPZ and LRSAM1 in Charcot-Marie-Tooth disease: Implications for genetic counseling for multi-gene panel testing

Detection of a novel complex rearrangement in KCNH2 with next-generation sequencing in a clinical laboratory

Genetic information for healthy individuals: Developing a medically actionable genetic screening panel


Glycine missense variants in the COL3A1 triple-helix domain: Assessing functional domain data during clinical variant interpretation

Harmonizing variant interpretation for sequence and copy number changes within individual genes in clinical diagnostic testing

Leveraging phenotype ontologies to improve variant interpretation by factoring in phenotype specificity

Metabolic pathognomonics: incorporating disease-specific biochemical data improves variant interpretation for inherited metabolic disorders

Molecular diagnosis of primary ciliary dyskinesia: Experience from a clinical laboratory

One of these things is not like the other: Clinically actionable discordance between germline sequencing and somatic tumor profiling in cancer patients

PMS2 pseudogene and disambiguation: Technically challenging, clinically critical

Potential of predispositional genetic screening for dominant actionable disorders: prevalence of genomic variants in 16,000 individuals

PRESENTATIONS

The spectrum of pathogenic variants underlying multiple conditions in 80,000 patients: Implications for test implementation, utilization and validation

Tracing the dark matter: Prevalence of copy number and structural variants across Mendelian disorders

2016 Posters and Presentations

American Society of Human Genetics (ASHG)

October 18-22, 2016
Vancouver BC

POSTERS

Accurate detection of copy-number changes in the highly conserved regions of PMS2 using NGS

Attitudes regarding personal genomic sequencing among healthy early adopters: Findings from the PeopleSeq Consortium

Creating a medically actionable genetic screening panel for healthy individuals

Evaluating the strength of evidence for gene-condition relationships: impact on multi-gene panel testing design

Germline hemizygous deletion of CDKN2A-CDKN2B locus in a patient presenting with Li-Fraumeni syndrome (also published in npj Genomics Medicine)

Glycine missense variants in the COL3A1 triple helix domain: assessing functional domain data during clinical variant interpretation

Mammalian species conservation data and the implication for clinical variant classification

Molecular follow-up of a newborn screening positive case of medium-chain acyl–coenzyme A dehydrogenase deficiency identified two ACADM variants:
Are they clinically pathogenic?

“Phenotypes of distinction”: When and how to integrate unique phenotypic information into variant interpretation

PseudoSlayer: Clinical-grade variant identification within segmental duplications using NGS data

“SMRTer Confirmation”: Scalable clinical read-through variant confirmation using the Pacific Biosciences SMRT® Sequencing platform

The spectrum of technically challenging pathogenic variants in patients presents new requirements for genetic test development and validation

Variant classifications are highly concordant in ClinVar but with variability in genes from different disease areas

What do public databases really tell us about classifications of variants in BRCA1 and BRCA2?

National Society of Genetic Counselors (NSGC)

September 28-OCTOBER 1, 2016
Seattle, Washington

POSTERS

Mammalian species conservation data and the implications for clinical variant classification

Novel large rearrangement of RAD51D in an ovarian and breast cancer family

Inherited cardiomyopathies in the pediatric population: what molecular testing reveals

presentations

Bioinformatics for genetic counselors, version 2.0

Creating a medically actionable genetic screening panel for healthy individuals

A novel approach to lab-based clinical genetic counseling

Hereditary genetic testing: current and future challenges

European Society of Human Genetics (ESHG)

May 21-24, 2016
Barcelona, Spain

poster

Copy number variation in clinical tests for inherited cardiomyopathies and arrhythmias

presentation

What have public databases taught us about variant classification?

Symposium on Hereditary Breast and Ovarian Cancer

May 10-13, 2016
Centre Mont-Royal, Montréal

posters

Variant classifications for BRCA1 and BRCA2 are substantially concordant across major clinical testing laboratories The expanding phenotype of PALB2-related cancer: clinical presentations of 144 identified carriers

presentation

Mosaic genetic variants in hereditary germline genetic testing: the expected and the unexpected

American Society of Breast Surgeons (ASBS)

April 13-17, 2016
Dallas, Texas

poster

Clinical presentation and management considerations for 77 breast cancer patients with germline PALB2 mutations

National Comprehensive Cancer Network® (NCCN)

March 31-April 2, 2016
Hollywood, FL

poster

Clinical actionability of panel tests for genes in the NCCN Guidelines for Hereditary Breast and Ovarian Cancer Clinical presentations of 111 patients with germline PALB2 mutations: Looking beyond breast and ovarian cancer

Society of Gynecologic Oncology (SGO)

March 19-22, 2016
San Diego, CA

poster

Preparing for the unexpected: Panel-based testing of ovarian cancer patients reveals actionable variants in non-canonical genes

Miami Breast Cancer Conference

March 10-13, 2016
Miami Beach, Florida

posters

Clinical actionability of non-BRCA1/2 mutations uncovered in multigene tests for hereditary breast cancer Variant classifications for BRCA1 and BRCA2 are highly concordant across major clinical testing laboratories Clinical presentation and management considerations for 68 breast cancer patients with germline PALB2 mutations

American College of Medical Genetics and Genomics (ACMG)

March 8-12, 2016
Tampa, Florida

posters

Allele frequency distribution of pathogenic sequence variants in ExAC and the implications for clinical genetic testing Expanding phenotypes of cancer predisposition genes: CDKN2A Detection of novel Alu insertions by next-generation sequencing of hereditary cancer genes Challenges of content expansion with panel testing: incorporating informatics into the clinical report Rare disease diagnosis obstacles: patient perspectives and physician findings To include or not to include: RASopathy genes in cardiomyopathy genetic testing To confirm or not to confirm, that is the question: a rigorous approach to evaluating the importance of Sanger confirmation of clinical NGS findings

presentation

Don't believe everything you hear: Variant classifications for BRCA1 and BRCA2 are highly concordant across major clinical testing laboratories

2015 Posters and Presentations

Association for Molecular Pathology (AMP)

November 5-7, 2015
Austin, TX

posters

An opportunity or dilemma? Customizable panel tests and clinician ordering behavior Establishing and evaluating a framework for describing variant evidence in clinical genomic reports Sherloc- Evaluation of a score-based implementation of the AMP-ACMG ISV guidelines in a scalable genetic diagnostic laboratory

Presentations

Analytic validation standards for NGS assays and new reference materials needed A rigorous approach to evaluating the importance of Sanger Confirmation of NGS findings
Clinical utility of NGS testing- Progress and challenges

National Society of Genetic Counselors (NSGC)

October 21-24, 2015
Pittsburgh, PA

posters

Clinical actionability of multigene tests for hereditary breast and ovarian cancer Integration of the ACMG ISV guidelines into clinical variant analysis and interpretation processes- A model for diagnostic standardization Moving beyond the 1%- incorporating the Exome Aggregation Consortium (ExAC) data into variant interpretation and classification To confirm or not confirm, that is the question: A rigorous approach to evaluating the importance of sanger confirmation of clinical NGS findings Understanding psychiatrists’ perceptions surrounding psychiatric genetics and genetic counseling services

Presentations

Finding just right- Balancing payer and provider goals for hereditary genetic testing Next generation sequencing- Challenges and strategies in testing patients with circulating hematopoietic malignancies Validation of clinical genetic tests - or – How to stop worrying and love the data!

American Society of Human Genetics (ASHG)

October 6-10, 2015
Baltimore, MD
Case series of colorectal cancer patients with BRCA 1/2 mutations: Finding actionable genes in patients with atypical presentations Sherloc: Evaluation of a scalable score-based implementation of the ACMG 2015 clinical variant interpretation guidelines To confirm or not confirm, that is the question: A rigorous approach to evaluating the importance of sanger confirmation of clinical NGS findings

Canadian Association of Genetic Counselors (CAGC)- Canadian College of Medical Geneticists (CCMG)

September 9-12, 2015
Ottawa, ON
Clinical actionability of multi-gene panel tests for hereditary breast and ovarian cancer (HBOC) Multiple pathogenic variants identified by next-generation sequencing hereditary cancer panel testing – a case report Colorectal cancer patients with BRCA 1 & BRCA 2 mutations- Preparing for unexpected results

RASopathies Conference

July 17-19, 2015
Seattle, WA
Case study of a large three-generation family with variable Noonan syndrome phenotypes Analysis of clinical indications, ordering behavior, and genetic testing results for Rasopathies genes and panels

American Society of Clinical Oncology (ASCO)

May 29-June 2, 2015
Chicago, IL
Clinical impact of multi-gene panel testing for hereditary breast and ovarian cancer risk assessment

ClinGen/DECIPHER

May 27-28, 2015
Washington, DC
The allele-frequency distribution of pathogenic sequence variants in ExAC

Mutation in the Genome sponsored by the Human Variome Project (HVP)

April 27-30, 2015
Leiden, Netherlands
Patterns of similarity and difference among clinical interpretations from multiple laboratories in ClinVar Traditional vs. next-generation panel testing of hereditary breast and ovarian cancer genes in a large clinical population Genome in a Bottle: You’ve sequenced. How well did you do?

American College of Medical Genetics and Genomics (ACMG) Annual Clinical Genetics Meeting

March 24-28, 2015
Salt Lake City, UT
Discovery and clinical interpretation of a SMAD4 retrotransposon using next-generation sequencing What do we do with VUS? Genetics professionals’attitudes toward reporting variants of uncertain significance Early-onset Charcot-Marie-Tooth disease with diaphragmatic weakness Next-generation panel vs. traditional testing of hereditary breast and ovarian cancer genes in a large clinical population An opportunity or dilemma? Customizable panel tests and clinician ordering behavior Sherloc: A weighted, score-based variant classification system based on the 2015 ACMG ISV guidelines

2014 Posters and Presentations

San Antonio Breast Cancer Symposium (SABCS)

December 9-13, 2014
San Antonio, TX
Technical evaluation of multi‐gene testing for hereditary breast and ovarian cancer Multi-gene panel testing for hereditary breast and ovarian cancer risk assessment

American Society of Hematology (ASH) Annual Meeting

December 6-9, 2014
San Francisco, CA
Clinical testing of five hereditary hemochromatosis‐related genes: Preliminary evidence for the benefit of Next-Generation Sequencing

Association for Molecular Pathology (AMP) Annual Meeting

November 12-15, 2014
National Harbor, MD
Development of a novel score based system for germline variant interpretation of clinical next-generation data Traditional vs. next-generation testing of hereditary breast and ovarian cancer genes in a large clinical population

Canadian Association of Genetic Counselors (CAGC) Annual Education Conference

November 4-8, 2014
Vancouver, BC, Canada
Clinical testing of five hereditary hemochromatosis‐related genes: Preliminary evidence for the benefit of Next-Generation Sequencing

The American Society of Human Genetics (ASHG) Annual Meeting

October 18-22, 2014
San Diego, CA
Clinical and technical evaluation of a multi-gene NGS panel for hereditary cancer risk assessment MLPAseq: Assaying genome copy number variation using MLPA paired with high-throughput sequencing Kragle: A new local de novo assembler and genotype caller for short tandem repeats and other complex variations Next-generation sequencing reveals a novel duplication in BRCA2

National Society of Genetic Counselors (NSGC) Annual Education Conference

September 17-20, 2014
New Orleans, LA
Next-generation sequencing reveals a novel duplication in BRCA2 Returning hereditary cancer panel research results is clinically feasible and appreciated by patients Rethinking the family cancer history questionnaire in the era of next generation sequencing panels - are we asking the right questions? Understanding next generation sequencing results: an update on elements of variant interpretation and classification Before it's too late - broad hereditary cancer panel testing at the end of life
Novel variant identified in CYP7B1 using next-generation sequencing A comparison of traditional and 29-gene panel testing for hereditary breast and ovarian cancer in over 1000 patients

Human Variome Project (HVP) Meeting

May 19, 2014
Paris, France
Clinical significance of transcript alignment discrepancies

American College of Medical Genetics and Genomics (ACMG) Annual Clinical Genetics Meeting

March 25-29, 2014
Nashville, TN
Heterogeneity of hereditary spastic paraplegia and the finding of phenotypic modifier variants
High accuracy and expanded yield from next-generation testing of multiple cancer genes
A low-cost, flexible diagnostic test for hundreds of inherited conditions

Miami Breast Cancer Conference

March 6-9, 2014
Miami, FL
High accuracy and expanded yield from next-generation testing of multiple cancer risk genes

Pacific Symposium on Biocomputing (PSB)

January 3-7, 2014
The Big Island, HI
CLINVITAE: An open database of clinically observed variants, and other open source tools from Invitae