File Name: copy number variation in human health disease and evolution .zip
Molecular methods, by which copy number variants CNVs detection is available, have been gradually introduced into routine diagnostics over the last 15 years. Despite this, some CNVs continue to be a huge challenge when it comes to clinical interpretation. CNVs are an important source of normal and pathogenic variants, but, in many cases, their impact on human health depends on factors that are not yet known. Therefore, perception of their clinical consequences can change over time, as our knowledge grows.
A computational tool to detect both germline and mosaic chromosomal alterations at low allelic fractions based on phased haplotype data. Mosaic chromsomal alterations in diploid cells affect the overall balance of alleles from the two haplotypes at consecutive heterozygous sites.
Long-range phase information allows the careful integration of this imbalance across long chromosomal segments. By carefully performing this integration, MoChA is capable of detecting mosaic chromosomal alterations present in as little as one percent of the cells that comprise the DNA library.
The ability to identify events at such low cell fractions greatly enhances the ability to detect clonality in samples from blood, cancer, and cell lines. MoChA is entirely written in C and based on HTSlib and BCFtools libraries and is equally capable of processing data from DNA microarray and whole-genome sequencing experiments, providing a simple unifying framework for researchers.
The mammalian brain is composed of diverse, specialized cell populations. To systematically ascertain and learn from these cellular specializations, we used Drop-seq to profile RNA expression in , individual cells sampled from 9 regions of the adult mouse brain.
We identified transcriptionally distinct groups of cells using computational approaches developed to distinguish biological from technical signals. Cross-region analysis of these cell populations revealed features of brain organization, including a gene-expression module for synthesizing axonal and presynaptic components, patterns in the co-deployment of voltage-gated ion channels, functional distinctions among the cells of the vasculature and specialization of glutamatergic neurons across cortical regions.
Systematic neuronal classifications for two complex basal ganglia nuclei and the striatum revealed a rare population of spiny projection neurons. This adult mouse brain cell atlas, accessible through interactive online software DropViz , serves as a reference for development, disease, and evolution. The complex variation of the complement component 4 C4 genes has prevented their effective inclusion in genome-wide studies based on SNP arrays and exome sequencing.
Here we provide resources to facilitate the analysis of C4 in both C4 -focused and genome-wide studies. Common C4 alleles can also be imputed from flanking SNPs.
Though recurring mutation at C4 makes imputation less effective than it is for simpler variants, we found that the common C4 alleles can generally be imputed with 0. Check back for updates: we are creating advanced reference panels from whole genome sequencing of much larger numbers of people, which we hope will enable the imputation of lower-frequency C4 alleles.
Molecular analysis of C4 structural variation using droplet digital PCR Reference panel for imputation Protocol for imputation. One of the first protein polymorphisms identified in humans involves the abundant blood protein haptoglobin. Two exons of the HP gene encoding haptoglobin exhibit copy number variation that affects HP protein structure and multimerization.
The evolutionary origins and medical relevance of this polymorphism have been uncertain. We showed that this variation has likely arisen from many recurring deletions, more specifically, reversions of an ancient hominin-specific duplication of these exons. Haptoglobin reference panel Paper: PDF. Human chromosome 17q Additionally, the inverted H2 form of 17q We developed a population genetics approach to analyze complex genome structures and identified nine segregating structural forms of 17q Both the H1 and H2 forms of the 17q An older H2 form lacking such a duplication is present at low frequency in European and central African hunter-gatherer populations.
We further showed that complex genome structures can be analyzed by imputation from SNPs. Protocol for reference panels Paper: PDF. Genome STRiP Genome STRucture In Populations is a set of software tools for analyzing genome structural variation in whole-genome sequence data from many individuals of the same species.
Bob Handsaker in our lab is the lead developer and architect. Bob Handsaker makes available his new maps of human genome copy number variation in the Genomes Project. These maps contain the genomic locations, alleles, and allele frequencies of 8, segregating CNVs in diverse populations, including 1, multi-allelic CNVs that are described for the first time at the levels of integer copy numbers, copy-number alleles, and allele frequencies.
These maps also report the relationships of CNV alleles to SNPs and haplotypes, including visual plots suitable for re-use in papers and presentations. Download data. Official Birdsuite website. Tell us about it! MOsaic CHromosomal Alterations MoChA Caller A computational tool to detect both germline and mosaic chromosomal alterations at low allelic fractions based on phased haplotype data. Mouse Brain Atlas The mammalian brain is composed of diverse, specialized cell populations.
Studying C4 The complex variation of the complement component 4 C4 genes has prevented their effective inclusion in genome-wide studies based on SNP arrays and exome sequencing. Schizophrenia risk from complex variation of complement component 4. Nature , Studying Haptoglobin One of the first protein polymorphisms identified in humans involves the abundant blood protein haptoglobin. Recurring exon deletions in the HP Haptoglobin gene contribute to lower blood cholesterol levels.
Nature Genetics , Studying the 17q Structural haplotypes and recent evolution of the human 17q Nature Genetic s, Large multiallelic copy number variations in humans. Handsaker et al. Discovery and genotyping of genome structural variation by sequencing on a population scale. Human genome replication timing DNA replication creates opportunities for mutation , and the timing of DNA replication correlates with the density of SNPs across the human genome.
Download data Koren et al. Differential relationship of DNA replication timing to different forms of human mutation and recombination. Am J Hum Gene t, Koren and McCarroll. Random replication of the inactive X chromosome. Genome Research , Koren et al. Genetic variation in human DNA replication timing. Cell , McCarroll et al. Korn et al. Macosko et al. Regan, Kamitaki et al.
PLoS One ,
Metrics details. Copy number variation CNV has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines, 6 3 MD-resistant and 7 2 MD-susceptible , as well as their F 1 generation and six recombinant congenic strains RCSs with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD. In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. Within these shared regions, harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 6 3 and 7 2 , respectively.
Copy number variation CNV can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1, genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. Several CNVs overlapping drug metabolism genes were verified with genomic quantitative polymerase chain reaction, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including 15 first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and 40 losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defense, inferring the genetic basis of its unique distribution in North Africa.
Protocol DOI: Copy number variation CNV , where a segment of DNA differs in copy number between different individuals, is an extensive and often underappreciated source of genetic variation within species. However, reliably determining copy number of a particular. However, reliably determining copy number of a particular DNA sequence for a large number of samples can be challenging. Here, I describe and review the paralogue ratio test PRT in detail. PRT was developed to robustly type the CNV of the beta-defensin locus using small amounts of genomic DNA in a high-throughput manner, and has been applied successfully at many other loci. I discuss the strategies for designing successful PRT assays using both manual and bioinformatics methods, how to optimize experimental conditions, and approaches for analyzing the data.
Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer.
Autism spectrum disorders ASDs are characterized by language impairments, social deficits, and repetitive behaviors. The onset of symptoms occurs by the age of 3 and shows a lifelong persistence. Genetics plays a major role in the etiology of ASD. Except genetics, several potential risk factors environmental factors and epigenetics may contribute to ASD.
Skip to search form Skip to main content You are currently offline. Some features of the site may not work correctly. DOI: Zhang and W. Gu and M.
Copy number variation CNV is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variations can be generally categorized into two main groups: short repeats and long repeats.
Your email address will not be published. Required fields are marked *