Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the exten...

Identifying causal relationships from observation data is difficult, in large part, due to the presence of hidden common causes. In some cases, where just the right patterns of conditional independence and dependence lie in the data—for example, Y-structures—it is possible to identify cause and effect. In other cases, the analyst deliberately makes an uncertain assumption that hidden common cau...

Mastitis is an inflammation-driven disease of the bovine mammary gland that occurs in response to physical damage or infection and is one of the most costly production-related diseases in the dairy industry worldwide. We performed a genome-wide association study (GWAS) to identify genetic loci associated with somatic cell score (SCS), an indicator trait of mammary gland inflammation. A total of...

The bovine leptin (LEP) gene was widely used as a candidate gene for molecular selection to improve productivity traits of cattle. This study was carried out to identify single nucleotide polymorphisms (SNPs) in the LEP gene of Sumba Ongole (SO, Bos indicus) cows using sequencing method. A total of 31 animals were used in this study for analyses. Research showed that total of 16 SNPs w...

background: it has been demonstrated that insulin signaling pathway related genes have important roles in polycystic ovary syndrome (pcos) risk. the goal of present investigation was to assess the potential association between insr/nsii (rs2059806) and insr/pmli (rs1799817) snps and pcos. methods: 50 women with pcos and 47 normal controls entered the study. nsii and pmli snps in the insr gene w...

Example 1. In a genetic study, n = 2217 patients are recruited, among which 1127 have bladder cancer. After whole genome sequencing, p = 475290 single nucleatide polymorphisms (or SNPs, a possible variation of the DNA sequence at one location) are measured on each patient. We construct a matrix X = (Xij)1≤i≤n,1≤j≤p where Xij = 1 if the ith patient has a mutation at jth location and 0 otherwise....

A somatic cell genome was recently resequenced for a patient with renal cancer. The data were submitted to the NCBI Sequence Read Archive under the accession number SRA012240. Here, we have performed SNP calling for the genome and compared it with several published genomes. We have found 2, 921, 724 SNPs, including 1, 472, 679 newly described ones. Among them, 63, 462 SNPs have been mapped to t...

The Hmong Diaspora is one of the widest modern human migrations. Mainly localised in South-East Asia, the United States of America, and metropolitan France, a small community has also settled the Amazonian forest of French Guiana. We have biologically analysed 62 individuals of this unique Guianese population through three complementary genetic markers: mitochondrial DNA (HVS-I/II and coding re...

BACKGROUND A large isoniazid-resistant tuberculosis outbreak centred on London, United Kingdom, has been ongoing since 1995. The aim of this study was to investigate the power and value of whole genome sequencing (WGS) to resolve the transmission network compared to current molecular strain typing approaches, including analysis of intra-host diversity within a specimen, across body sites, and o...