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Open AccessJournal ArticleDOI

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists

Marilyn M. Li, +10 more
- 01 Jan 2017 - 
- Vol. 19, Iss: 1, pp 4-23
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TLDR
A four-tiered system to categorize somatic sequence variations based on their clinical significances is proposed, with variants with strong clinical significance and variants with potential clinical significance in tier I; tier III, variants of unknown clinical significance; and tier IV, variants deemed benign or likely benign.
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This article is published in The Journal of Molecular Diagnostics.The article was published on 2017-01-01 and is currently open access. It has received 1113 citations till now.

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Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic

Timothy A. Chan, +6 more
- 01 Jan 2019 - 
TL;DR: TMB, in concert with PD-L1 expression, has been demonstrated to be a useful biomarker for ICB selection across some cancer types; however, further prospective validation studies are required.
Journal ArticleDOI

Human primary liver cancer–derived organoid cultures for disease modeling and drug screening

Laura Broutier, +21 more
- 13 Nov 2017 - 
TL;DR: The wide-ranging biomedical utilities of PLC-derived organoid models in furthering the understanding of liver cancer biology and in developing personalized-medicine approaches for the disease are demonstrated.
Journal ArticleDOI

Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology

Neal I. Lindeman, +21 more
- 01 Mar 2018 - 
TL;DR: The 2013 guideline for molecular analysis of lung cancers was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing.
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Circulating Tumor DNA Analysis in Patients With Cancer: American Society of Clinical Oncology and College of American Pathologists Joint Review

Jason D. Merker, +16 more
- 05 Mar 2018 - 
TL;DR: There is no evidence of clinical validity and clinical utility to suggest that ctDNA assays are useful for cancer screening, outside of a clinical trial, and re-evaluation of the literature will shortly be required.
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Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

Michael R. Wilson, +42 more
- 13 Jun 2019 - 
TL;DR: Routine microbiologic testing is often insufficient to detect all neuroinvasive pathogens, so metagenomic NGS of CSF obtained from patients with meningitis or encephalitis improved diagnosis of neurologic infections and provided actionable information in some cases.
References
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Journal ArticleDOI

The Sequence Alignment/Map format and SAMtools

Heng Li, +8 more
- 01 Aug 2009 - 
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Sue Richards, +12 more
- 05 Mar 2015 - 
TL;DR: Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends thatclinical molecular genetic testing should be performed in a Clinical Laboratory Improvement Amendments–approved laboratory, with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or the equivalent.
Journal ArticleDOI

A global reference for human genetic variation.

Adam Auton, +517 more
- 01 Oct 2015 - 
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Journal ArticleDOI

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal

Jianjiong Gao, +12 more
- 02 Apr 2013 - 
TL;DR: A practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics, which makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries.
Journal ArticleDOI

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

Pablo Cingolani, +8 more
- 01 Apr 2012 - 
TL;DR: It appears that the 5′ and 3′ UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus.
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