Detection of de novo copy number alterations in case-parent trios using the R package MinimumDistance

Finding de novo copy number variants in case-parent trios for oral clefts

Imputation of parent-offspring trios and their effect on accuracy of genomic prediction using Bayesian method

The objective of this study was to evaluate the imputation accuracy of parent-offspring trios under different scenarios. By using simulated datasets, the performance Bayesian LASSO in genomic prediction was also examined. The genome consisted of 5 chromosomes and each chromosome was set as 1 Morgan length. The number of SNPs per chromosome was 10000. One hundred QTLs were randomly distributed a...

Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data.

RATIONALE Congenital heart disease (CHD) is among the most common birth defects. Most cases are of unknown pathogenesis. OBJECTIVE To determine the contribution of de novo copy number variants (CNVs) in the pathogenesis of sporadic CHD. METHODS AND RESULTS We studied 538 CHD trios using genome-wide dense single nucleotide polymorphism arrays and whole exome sequencing. Results were experime...

Microduplication of Xp22.31 and MECP2 Pathogenic Variant in a Girl with Rett Syndrome: A Case Report

Rett syndrome (RS) is a neurodevelopmental infantile disease characterized by an early normal psychomotor development followed by a regression in the acquisition of normal developmental stages. In the majority of cases, it leads to a sporadic mutation in the MECP2 gene, which is located on the X chromosome. However, this syndrome has also been associated with microdeletions, gene translocations...

Copy number variation detection and genotyping from exome sequence data.

While exome sequencing is readily amenable to single-nucleotide variant discovery, the sparse and nonuniform nature of the exome capture reaction has hindered exome-based detection and characterization of genic copy number variation. We developed a novel method using singular value decomposition (SVD) normalization to discover rare genic copy number variants (CNVs) as well as genotype copy numb...