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Estimating IBD tracts from low coverage NGS data
2016
Bioinformatics
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Results: Here, we present a new method for estimating inbreeding IBD tracts from low coverage NGS data. ...
We benchmark it under a wide range of biologically relevant conditions and show that the new method provides a marked increase in accuracy even at low coverage. ...
The method presented here facilitates the estimation of IBD tracts from low coverage NGS data. We evaluate its performance through both simulated and real data analyses. ...
doi:10.1093/bioinformatics/btw212
pmid:27153648
fatcat:edqelkwunbcnnguzhkmgsmzdnq
The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population
2015
Genetics
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Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia ...
Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. ...
Acknowledgments We thank Stephen Richards for assistance with the DGRP data; J. J. ...
doi:10.1534/genetics.115.174664
pmid:25631317
pmcid:PMC4391556
fatcat:mcxnxawuuvan5jbo3t2rjtgls4
Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
2013
Genome Research
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Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. ...
For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F ) for each individual before calling genotypes. ...
Results Estimating per-site inbreeding coefficients from simulated data During standard NGS data analyses, one of the most crucial steps is quality control. ...
doi:10.1101/gr.157388.113
pmid:23950147
pmcid:PMC3814885
fatcat:kvs76uhdqzfidfc7ifckyzm2c4
Using Haplotype Information for Conservation Genomics
2019
Trends in Ecology & Evolution
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Beyond allele frequencies, haplotype data collected in population samples contain information about the history of allelic associations in gene genealogies, and this is of tremendous potential for conservation ...
One main advantage of these methods is that phased data are not needed, and they are also appropriate for low-coverage or pool-sequencing data [84, 101] . ...
(i) Indirect approaches [31, 32] can use short-read NGS data from related or unrelated individuals. ...
doi:10.1016/j.tree.2019.10.012
pmid:31810774
fatcat:tuv56pehefhz5nx2t2tjf545du
The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria
2019
eLife
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Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates the number of strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes ...
Finally, leveraging data from the Malaria Atlas Project, we find that prevalence correlates within Africa, but not Asia, with both the rate of mixed infection and the level of IBD. ...
Grey points identify experiments of low coverage data (median sequencing depth < 20), and pink identify cases where K is inferred incorrectly. ...
doi:10.7554/elife.40845
pmid:31298657
pmcid:PMC6684230
fatcat:affedltabrf2xoksrpx5narv6m
Inflammatory bowel disease epidemiology in São Paulo State, Brazil
2018
Clinical and Experimental Gastroenterology
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This study aimed to estimate the incidence and prevalence of inflammatory bowel disease (IBD) in São Paulo, Brazil, for 2012-2015. ...
The demographic and clinical data, such as age and sex, were collected for each patient. ...
Introduction Inflammatory bowel disease (IBD) is characterized by an inflammatory process that compromises the digestive tract, partially or totally. ...
doi:10.2147/ceg.s176583
pmid:30464570
pmcid:PMC6214600
fatcat:ed3zwodlw5bglg47rzng3jdwga
Complete Genes May Pass from Food to Human Blood
2013
PLoS ONE
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Our bloodstream is considered to be an environment well separated from the outside world and the digestive tract. ...
Here, based on the analysis of over 1000 human samples from four independent studies, we report evidence that meal-derived DNA fragments which are large enough to carry complete genes can avoid degradation ...
Author Contributions Figure 1 . 1 Coverage of the tomato chloroplast in the IBD sample. ...
doi:10.1371/journal.pone.0069805
pmid:23936105
pmcid:PMC3728338
fatcat:hsj7pukuzrhhzcpv2jtiqnoigm
Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
2012
PLoS Genetics
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Most genomes were sequenced above 25X depth from haploid embryos. ...
Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. ...
occurred outside recurrent IBD regions, or when tracts greater than 5 Mb overlapped recurrent IBD regions. ...
doi:10.1371/journal.pgen.1003080
pmid:23284287
pmcid:PMC3527209
fatcat:jf3qbje5crfrbfttoco4osjdbe
A metagenomic DNA sequencing assay that is robust against environmental DNA contamination
[article]
2021
biorxiv/medrxiv
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We applied Coffee-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial ...
Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass ...
.), R37 AI051652 (to M.S), a Synergy award from the Rainin Foundation (to I.D.V. and R.L.), a grant from the Bill and Melinda Gates ...
doi:10.1101/2021.11.22.469599
pmid:34845444
pmcid:PMC8629186
fatcat:trh6nrf4vfb7hjuwwgozid745u
HAPLOTYPE PHASING BY MULTI-ASSEMBLY OF SHARED HAPLOTYPES: PHASE-DEPENDENT INTERACTIONS BETWEEN RARE VARIANTS
[chapter]
2010
Biocomputing 2011
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Results are presented in Sec. 2. (2) In Sec. 3, we present algorithmic strategies for haplotype assembly using NGS, NGS + genotype data, and NGS + pedigree information. (3) This work builds on algorithms ...
In this paper we propose algorithmic strategies, Lander-Waterman-like statistical estimates, and genome-wide software for haplotype phasing by multi-assembly of shared haplotypes. ...
These estimates could provide valuable insight when deciding sequence coverage per individual in association studies employing NGS technology. ...
doi:10.1142/9789814335058_0010
fatcat:kj6mi47bmrelhmfcb2rhknvt3i
Mountain lion genomes provide insights into genetic rescue of inbred populations
[article]
2018
bioRxiv
pre-print
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However, the genome of an admixed Florida panther that descended from a translocated individual from Central America had surprisingly long tracts of homozygosity, indicating that genomic gains from translocation ...
Tracts of homozygosity were rarely shared among populations, suggesting that assisted gene flow would restore local genetic diversity. ...
Webber from the Paleogenomics lab, and C. Scelfo-Dalbey for assistance in generating data. ...
doi:10.1101/482315
fatcat:hasvfolipbfdvdqsuzqshlidpe
Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease
2011
Nature Genetics
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Crohn's disease (CD) and ulcerative colitis (UC) are classified as chronic, idiopathic inflammatory bowel diseases (IBD) of the gastrointestinal tract with unknown etiology (IBD: OMIM #266600). ...
of rare and low frequency variants discovered, power evaluation and QC summary, and annotation of variants discovered in regions from primary sequencing data in BAM/SAM format. ...
doi:10.1038/ng.952
pmid:21983784
pmcid:PMC3378381
fatcat:qwkndwnihraqtonbwf2a2aiefy
High-resolution single-cell sequencing of malaria parasites
[article]
2017
bioRxiv
pre-print
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Targeting of these cells routinely generates near-complete capture of the 23Mb P. falciparum genome (mean breadth of coverage 90.7%) at high efficiency. ...
Here, we demonstrate that parasites in late cell cycle stages, which contain increased DNA content, are far superior templates for generating high quality genomic data. ...
As this tool was designed for diploid data we generated doubled homozygotes and collapsing together overlapping estimates of IBD. ...
doi:10.1101/130864
fatcat:saxdziepnbfzniptkfgx6usgc4
Genomic analysis of the blood attributed to Louis XVI (1754–1793), king of France
2014
Scientific Reports
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We sequenced the complete genome of the DNA contained in the gourd at low coverage (,2.53) with coding sequences enriched at a higher ,7.33 coverage. ...
From a functional perspective, we did not find an excess of alleles contributing to height despite being described as the tallest person in Court. ...
., and a predoctoral fellowship from the Basque Government (DEUI) to I.O. ...
doi:10.1038/srep04666
pmid:24763138
pmcid:PMC3998215
fatcat:7wunjwzpuzbfvee5lnthfd33t4
A single nucleotide polymorphism in dopamine beta hydroxylase (rs6271(C>T)) is over-represented in inflammatory bowel disease patients and reduces circulating enzyme
2019
PLoS ONE
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Seven SNPs were observed from DβH targeted exome sequencing in the 45 IBD patients. ...
IBD patients were screened by targeted exome sequencing and compared with NeuroX DβH single nucleotide polymorphism (SNP) genotyping data of the controls. ...
C) The distribution of DβH quantity in both study cohorts as estimated from ELISA assays. ...
doi:10.1371/journal.pone.0210175
pmid:30817802
pmcid:PMC6394932
fatcat:cw365qujxndsdl457mu67stg74
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