A High-Resolution Map of Segmental DNA Copy Number Variation in the Mouse Genome

Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits

DNA sequence variation and haplotype structure of the ICAM1 and TNF genes in 12 ethnic groups of India reveal patterns of importance in designing association studies

We have examined the patterns of DNA sequence variation in and around the genes coding for ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India. We aimed to (a) quantify the nature and extent of the variation, and (b) analyse the observed patterns of variation in relation to population history and ethnic background. At the ICAM1 and TNF loci, respectively, the total numbers of SNPs that were detected were 28 and 12. Many of these SNPs are not shared across ethnic groups and are unreported in the dbSNP or TSC databases, including two fairly common non-synonymous SNPs at positions 13487 and 13542 in the ICAM1 gene. Conversely, the TNF-376A SNP that is reported to be associated with susceptibility to malaria was not found in our study populations, even though some of the populations inhabit malaria endemic areas. Wide between-population variation in the frequencies of shared SNPs and coefficients of linkage disequilibrium have been observed. These findings have profound implications in case-control association studies

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

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Insertion/Deletion Polymorphisms in Tribal Populations of Southern India and Their Possible Evolutionary Implications

India has the unique distinction of having perhaps the largest diversities, both biological and cultural. The Nilgiri Hills of southern India, a home for several tribal pockets representing different genetic isolates, pro- vides a genetic wealth to understand human evolution. We have analyzed eight widely distributed polymorphic insertion/deletion loci (AluAPO, Alu- ACE, AluD1, AluPLAT, AluPV92, AluFXIIIB, CD4 del and mtNUC) in 250 unrelated individuals from five tribal populations (Badaga, Irula, Kota, Ku- rumba, and Toda). All loci were highly polymorphic except the CD4 del lo- cus, at which the deletion allele was fixed in Kotas and Kurumbas. The levels of average heterozygosities were found to be high in all the populations. In most populations, they were also higher than those predicted by the island model of population structure. The gene diversity (GST = 8.3%) was found to be higher than that in populations of most global regions with the exception of Africa. It is clear from the present study that drift effects could have ac- centuated the process of genetic differentiation of the tribal populations. The possibility of an early demographic expansion of modern humans within south India also cannot be ruled out

A survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus in the Nilgiri hill tribes, South India

DNA analysis has made it easier to study haplotypes, arrays of alleles at closely linked loci along the chromosome. These regions are short enough to show little or no recombination, and behave as blocks that might have ancient origins. Scoring these markers as haplotypes, allows analysis both in terms of haplotype frequencies and identity in terms of linkage disequilibrium. The human dopaminergic system is an important focus of study in the fields of neuropsychiatry and pharmacology; it is also a promising nuclear DNA marker in studies of human genome diversity. Haplotype frequencies and linkage disequilibrium for the dopamine D2 receptor gene (DRD2) was determined in 250 unrelated individuals from five tribal populations. The three marker systems in this study are highly polymorphic in all the five tribal populations and the haplotype system showed high level of heterozygosities. Out of the possible eight haplotypes, four are commonly shared by all the populations. The ancestral allele B2D2A1 accounts for 0.021 to 0.080, which was present in all the groups consistently. The linkage disequilibrium was statistically significant in all the populations. Data obtained in this study on DRD2 represent one of the small, but growing number of data sets examining disequilibrium and haplotype frequencies in human populations

Mitochondrial DNA diversity among five tribal populations of Southern India

DNA samples from 160 unrelated individuals belonging to five Dravidian tribal populations of southern India were analysed for ten mitochondrial DNA(mtDNA) restriction site polymorphisms (RSPs) and one insertion/deletion polymorphism. There is extensive sharing of mtDNA haplotypes among all the tribal populations studied, indicating that there was a small femal founding population in India. The 9-bp deletion analysed was observed only in the Kadar population with a low frequency. The Asian-specific haplogroup M is found at a higher frequency in all the populations, thus supporting the hypothesis that this haplogroup U is also found in all the populations and it is consistent with the theory that Dravidian-speaking populations were more wide-spread in India and that the Aryan-speakers pushed them to their present habitat

Text Data Transfer Using Li-Fi Communication

A new and innovative technology called Light Fidelity (Li-Fi) has been developed in the past few years which are an alternate solution for wireless fidelity (Wi-Fi). Li-Fi uses light source as a transmitting medium for data transmission. The data is transmitted by flickering the light source (i.e. switching them On and Off) at a speed that cannot be noticeable to the eye. In this proposed article, wireless data transfer b e t w e e n t w o systems is established with the support of Li-Fi technology. Here data is transmitted from Tx PC via the LASER module that is driven by the Arduino UNO. On the receiver side data will be received on Rx PC using the photodiode (Solar panel), which is also connected to the Arduino UNO to extract the original data from the light. Li-Fi provides better bandwidth, efficiency, connectivity and security than WiFi and achieved high speeds larger than 1 Gbps under the laboratory conditions. The experimental report shows that the bit rate is enhanced using the proposed system and reached up to 147 bps with 1 0 0 % accuracy, over a 50 cm di sta nc e . And the setup also made it simpler than others out there and overall cost also reduce