Analysis of concordance of different haplotype block partitioning algorithms

BACKGROUND: Different classes of haplotype block algorithms exist and the ideal dataset to assess their performance would be to comprehensively re-sequence a large genomic region in a large population. Such data sets are expensive to collect. Alternatively, we performed coalescent simulations to generate haplotypes with a high marker density and compared block partitioning results from diversity based, LD based, and information theoretic algorithms under different values of SNP density and allele frequency. RESULTS: We simulated 1000 haplotypes using the standard coalescent for three world populations – European, African American, and East Asian – and applied three classes of block partitioning algorithms – diversity based, LD based, and information theoretic. We assessed algorithm differences in number, size, and coverage of blocks inferred under different conditions of SNP density, allele frequency, and sample size. Each algorithm inferred blocks differing in number, size, and coverage under different density and allele frequency conditions. Different partitions had few if any matching block boundaries. However they still overlapped and a high percentage of total chromosomal region was common to all methods. This percentage was generally higher with a higher density of SNPs and when rarer markers were included. CONCLUSION: A gold standard definition of a haplotype block is difficult to achieve, but collecting haplotypes covered with a high density of SNPs, partitioning them with a variety of block algorithms, and identifying regions common to all methods may be the best way to identify genomic regions that harbor SNP variants that cause disease

Association of TMTC2 with human nonsyndromic sensorineural hearing loss

IMPORTANCE: Sensorineural hearing loss (SNHL) is commonly caused by conditions that affect cochlear structures or the auditory nerve, and the genes identified as causing SNHL to date only explain a fraction of the overall genetic risk for this debilitating disorder. It is likely that other genes and mutations also cause SNHL. OBJECTIVE: To identify a candidate gene that causes bilateral, symmetric, progressive SNHL in a large multigeneration family of Northern European descent. DESIGN, SETTING, AND PARTICIPANTS: In this prospective genotype and phenotype study performed from January 1, 2006, through April 1, 2016, a 6-generation family of Northern European descent with 19 individuals having reported early-onset hearing loss suggestive of an autosomal dominant inheritance were studied at a tertiary academic medical center. In addition, 179 unrelated adult individuals with SNHL and 186 adult individuals reporting nondeafness were examined. MAIN OUTCOMES AND MEASURES: Sensorineural hearing loss. RESULTS: Nine family members (5 women [55.6%]) provided clinical audiometric and medical records that documented hearing loss. The hearing loss is characterized as bilateral, symmetric, progressive SNHL that reached severe to profound loss in childhood. Audiometric configurations demonstrated a characteristic dip at 1000 to 2000 Hz. All affected family members wear hearing aids or have undergone cochlear implantation. Exome sequencing and linkage and association analyses identified a fully penetrant sequence variant (rs35725509) on chromosome 12q21 (logarithm of odds, 3.3) in the TMTC2 gene region that segregates with SNHL in this family. This gene explains the SNHL occurrence in this family. The variant is also associated with SNHL in a cohort of 363 unrelated individuals (179 patients with confirmed SNHL and 184 controls, P = 7 x 10-4). CONCLUSIONS AND RELEVANCE: A previously uncharacterized gene, TMTC2, has been identified as a candidate for causing progressive SNHL in humans. This finding identifies a novel locus that causes autosomal dominant SNHL and therefore a more detailed understanding of the genetic basis of SNHL. Because TMTC2 has not been previously reported to regulate auditory function, the discovery reveals a potentially new, uncharacterized mechanism of hearing loss

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

As a consequence of the accumulation of insertion events over evolutionary time, mobile elements now comprise nearly half of the human genome. The Alu, L1, and SVA mobile element families are still duplicating, generating variation between individual genomes. Mobile element insertions (MEI) have been identified as causes for genetic diseases, including hemophilia, neurofibromatosis, and various cancers. Here we present a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data of 185 samples in three major populations detected with two detection methods. This catalog enables us to systematically study mutation rates, population segregation, genomic distribution, and functional properties of MEI polymorphisms and to compare MEI to SNP variation from the same individuals. Population allele frequencies of MEI and SNPs are described, broadly, by the same neutral ancestral processes despite vastly different mutation mechanisms and rates, except in coding regions where MEI are virtually absent, presumably due to strong negative selection. A direct comparison of MEI and SNP diversity levels suggests a differential mobile element insertion rate among populations

Effect of Bombay high crude oil and its water-soluble fraction on growth and metabolism of diatom Thalassiosira sp.

251-255Effect of Bombay high crude oil (BHC) and its water-soluble fraction (WSF) on growth and metabolism of the phytoplankton, Thalassiosira sp. was assessed. The study revealed the signs of acute toxicity at higher concentrations of crude oil (0.5%) and WSF (40%), while stimulatory effect was observed at lower concentrations (0.01 and 0.1% of BHC and 5, 10% of WSF). WSF at higher concentrations (20 and 40%) caused reduction in DNA and RNA of the diatom. At lower concentrations it caused increase in protein and RNA content indicating increased metabolism. High concentrations of oil and its fraction had inhibitory effect on growth, protein content and nucleic acid content. This indicates that biosynthesis of these molecules may be probable targets for toxicity of oil

In vitro screening for antitumour activity of Clinopodium vulgare L. (Lamiaceae) extracts.

Aqueous extract of Clinopodium vulgare L. showed strong antitumour activity when tested in vitro on A2058 (human metastatic melanoma), HEp-2 (epidermoid carcinoma, larynx, human) and L5178Y (mouse lymphoma) cell lines-6 h after treatment disintegration of the nuclei and cell lysis started. Applied at a concentration of 80 microg/ml it reduced the cell survival to 1.0, 5.6 and 6.6%, respectively. The concentrations of aqueous extract inhibiting the growth of A2058, HEp-2 and L5178Y cells by 50% (IC50 values) were calculated to be 20, 10 and 17.8 microg/ml respectively. Two groups of active substances were detected: the first one, probably combining glycosides, influenced adhesion, while the second one caused massive cell vacuolisation. The chloroform extract, which contained ursolic acid and gentriacontan had also cytotoxic, however a little bit weaker effect. All changes observed were irreversible