Joint detection of copy number variations in parent-offspring trios

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

For the analysis of case-parent trio genotyping arrays, copy number variants (CNV) appearing in the offspring that differ from the parental copy numbers are often of interest (de novo CNV). This package defines a statistic, referred to as the minimum distance, for identifying de novo copy number alterations in the offspring. We smooth the minimum distance using the circular binary segmentation ...

Genotype calling and haplotyping in parent-offspring trios.

Emerging sequencing technologies allow common and rare variants to be systematically assayed across the human genome in many individuals. In order to improve variant detection and genotype calling, raw sequence data are typically examined across many individuals. Here, we describe a method for genotype calling in settings where sequence data are available for unrelated individuals and parent-of...

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...

Detection of germline and somatic copy number variations in cattle.

As a complement to the Bovine HapMap Consortium project, we initiated a systematic study of the copy numbervariation (CNV) within the same cattle population using array comparative genomic hybridization (array CGH). Oligonucleotide CGH arrays were designed and fabricated to cover all chromosomes with an average interval of 6 kb using the latest bovine genome assembly. In the initial screening, ...