A survey of tools for variant analysis of next-generation genome sequencing data

S Pabinger, A Dander, M Fischer…�- Briefings in�…, 2014 - academic.oup.com
Recent advances in genome sequencing technologies provide unprecedented opportunities
to characterize individual genomic landscapes and identify mutations relevant for diagnosis�…

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

GM Cooper, J Shendure�- Nature Reviews Genetics, 2011 - nature.com
Genome and exome sequencing yield extensive catalogues of human genetic variation.
However, pinpointing the few phenotypically causal variants among the many variants�…

[HTML][HTML] Exome sequencing and analysis of 454,787 UK Biobank participants

JD Backman, AH Li, A Marcketta, D Sun, J Mbatchou…�- Nature, 2021 - nature.com
A major goal in human genetics is to use natural variation to understand the phenotypic
consequences of altering each protein-coding gene in the genome. Here we used exome�…

[HTML][HTML] REVEL: an ensemble method for predicting the pathogenicity of rare missense variants

NM Ioannidis, JH Rothstein, V Pejaver…�- The American Journal of�…, 2016 - cell.com
The vast majority of coding variants are rare, and assessment of the contribution of rare
variants to complex traits is hampered by low statistical power and limited functional data�…

Association analysis identifies 65 new breast cancer risk loci

K Michailidou, S Lindstr�m, J Dennis, J Beesley, S Hui…�- Nature, 2017 - nature.com
Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as
BRCA1, and many common, mostly non-coding variants. However, much of the genetic�…

[HTML][HTML] Genomic and molecular landscape of DNA damage repair deficiency across the cancer genome atlas

TA Knijnenburg, L Wang, MT Zimmermann…�- Cell reports, 2018 - cell.com
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic
response. We systematically analyzed somatic alterations to provide a comprehensive view�…

[HTML][HTML] ACE2 and TMPRSS2 variants and expression as candidates to sex and country differences in COVID-19 severity in Italy

R Asselta, EM Paraboschi, A Mantovani…�- Aging (albany NY), 2020 - ncbi.nlm.nih.gov
As the outbreak of coronavirus disease 2019 (COVID-19) progresses, prognostic markers for
early identification of high-risk individuals are an urgent medical need. Italy has one of the�…

Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity

P Akbari, A Gilani, O Sosina, JA Kosmicki, L Khrimian…�- Science, 2021 - science.org
INTRODUCTION Obesity accounts for a substantial and growing burden of disease globally.
Body adiposity is highly heritable, and human genetic studies can lead to biological and�…

dbNSFP v3. 0: A one‐stop database of functional predictions and annotations for human nonsynonymous and splice‐site SNVs

X Liu, C Wu, C Li, E Boerwinkle�- Human mutation, 2016 - Wiley Online Library
The purpose of the dbNSFP is to provide a one‐stop resource for functional predictions and
annotations for human nonsynonymous single‐nucleotide variants (nsSNVs) and splice‐site�…

[HTML][HTML] dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

X Liu, C Li, C Mou, Y Dong, Y Tu�- Genome medicine, 2020 - Springer
Whole exome sequencing has been increasingly used in human disease studies.
Prioritization based on appropriate functional annotations has been used as an�…