[HTML][HTML] Best practices for variant calling in clinical sequencing

DC Koboldt - Genome Medicine, 2020 - Springer
Next-generation sequencing technologies have enabled a dramatic expansion of clinical
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …

MET-dependent solid tumours—molecular diagnosis and targeted therapy

R Guo, J Luo, J Chang, N Rekhtman, M Arcila… - Nature reviews Clinical …, 2020 - nature.com
Attempts to develop MET-targeted therapies have historically focused on MET-expressing
cancers, with limited success. Thus, MET expression in the absence of a genomic marker of …

GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data

M Babadi, JM Fu, SK Lee, AN Smirnov, LD Gauthier… - Nature …, 2023 - nature.com
Copy number variants (CNVs) are major contributors to genetic diversity and disease. While
standardized methods, such as the genome analysis toolkit (GATK), exist for detecting short …

[HTML][HTML] CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing

E Talevich, AH Shain, T Botton… - PLoS computational …, 2016 - journals.plos.org
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are
of significant importance in syndromic conditions and cancer. Massively parallel sequencing …

The role of exome sequencing in newborn screening for inborn errors of metabolism

AN Adhikari, RC Gallagher, Y Wang, RJ Currier… - Nature medicine, 2020 - nature.com
Public health newborn screening (NBS) programs provide population-scale ascertainment
of rare, treatable conditions that require urgent intervention. Tandem mass spectrometry …

Tissue-specific mutation accumulation in human adult stem cells during life

F Blokzijl, J De Ligt, M Jager, V Sasselli, S Roerink… - Nature, 2016 - nature.com
The gradual accumulation of genetic mutations in human adult stem cells (ASCs) during life
is associated with various age-related diseases, including cancer,. Extreme variation in …

Recent ultra-rare inherited variants implicate new autism candidate risk genes

AB Wilfert, TN Turner, SC Murali, PH Hsieh… - Nature …, 2021 - nature.com
Autism is a highly heritable complex disorder in which de novo mutation (DNM) variation
contributes significantly to risk. Using whole-genome sequencing data from 3,474 families …

The ExAC browser: displaying reference data information from over 60 000 exomes

KJ Karczewski, B Weisburd, B Thomas… - Nucleic acids …, 2017 - academic.oup.com
Worldwide, hundreds of thousands of humans have had their genomes or exomes
sequenced, and access to the resulting data sets can provide valuable information for …

[HTML][HTML] A prospective study of sudden cardiac death among children and young adults

RD Bagnall, RG Weintraub, J Ingles… - … England Journal of …, 2016 - Mass Medical Soc
Background Sudden cardiac death among children and young adults is a devastating event.
We performed a prospective, population-based, clinical and genetic study of sudden cardiac …

Sequencing depth and coverage: key considerations in genomic analyses

D Sims, I Sudbery, NE Ilott, A Heger… - Nature Reviews …, 2014 - nature.com
Sequencing technologies have placed a wide range of genomic analyses within the
capabilities of many laboratories. However, sequencing costs often set limits to the amount …