Enhancing power of rare variant association test by Zoom-Focus Algorithm (ZFA) to locate optimal testing region [PDF]
arXiv, 2016 Motivation: Exome or targeted sequencing data exerts analytical challenge to test single nucleotide polymorphisms (SNPs) with extremely small minor allele frequency (MAF). Various rare variant tests were proposed to increase power by aggregating SNPs within a fixed genomic region, such as a gene or pathway. However, a gene could contain from several to
arxiv
Signaling Network Assessment of Mutations and Copy Number Variations Predicts Breast Cancer Subtype-specific Drug Targets [PDF]
, 2014 Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed exome-sequencing on several breast cancer cell lines which represent two subtypes, luminal and basal.
arxiv +1 more source
PCR-free whole exome sequencing: Cost-effective and efficient in detecting rare mutations.
PLoS ONE, 2019 In this study, we describe the development of a PCR-free whole exome sequencing method. Using this method, 2 μg DNA was sufficient for library preparation for whole exome sequencing.
Izumi Yamaguchi +3 more
doaj +1 more source
Whole exome sequencing in the rat
BMC Genomics, 2018 Background The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation.
Julie F. Foley +15 more
doaj +1 more source
Orphanet Journal of Rare Diseases, 2023 Intellectual disability (ID) has a prevalence of 1–3% and aproximately 30–50% of ID cases have a genetic cause. Development of next-generation sequencing has shown a high diagnostic potential.
María Juliana Ballesta-Martínez +8 more
doaj +1 more source
Predicting discovery rates of genomic features [PDF]
arXiv, 2014 Successful sequencing experiments require judicious sample selection. However, this selection must often be performed on the basis of limited preliminary data. Predicting the statistical properties of the final sample based on preliminary data can be challenging, because numerous uncertain model assumptions may be involved.
arxiv
A New Statistical Framework for Genetic Pleiotropic Analysis of High Dimensional Phenotype Data [PDF]
arXiv, 2015 The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high dimensional genotype (next-generation sequencing) data. To overcome these limitations, we develop sparse structural equation
arxiv
Multivariate Functional Regression Models for Epistasis Analysis [PDF]
arXiv, 2015 To date, most genetic analyses of phenotypes have focused on analyzing single traits or, analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power, and hold the key to understanding the complicated genetic structure of the complex diseases.
arxiv
High burden of private mutations due to explosive human population growth and purifying selection [PDF]
arXiv, 2014 Recent studies have shown that human populations have experienced a complex demographic history, including a recent epoch of rapid population growth that led to an excess in the proportion of rare genetic variants in humans today. This excess can impact the burden of private mutations for each individual, defined here as the proportion of heterozygous ...
arxiv
A W-test collapsing method for rare variant testing with applications to exome sequencing data of hypertensive disorder [PDF]
arXiv, 2016 Advancement in sequencing technology enables the study of association between complex disorders and rare variants with low minor allele frequencies. One of the major challenges in rare variant testing is lack of statistical power of traditional testing methods due to extremely low variances of single nucleotide polymorphisms.
arxiv