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Estimating IBD tracts from low coverage NGS data

Filipe G. Vieira, Anders Albrechtsen, Rasmus Nielsen
2016 Bioinformatics  
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

Justin B. Lack, Charis M. Cardeno, Marc W. Crepeau, William Taylor, Russell B. Corbett-Detig, Kristian A. Stevens, Charles H. Langley, John E. Pool
2015 Genetics  
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  Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations.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

Filipe G. Vieira, Matteo Fumagalli, Anders Albrechtsen, Rasmus Nielsen
2013 Genome Research  
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

Maeva Leitwein, Maud Duranton, Quentin Rougemont, Pierre-Alexandre Gagnaire, Louis Bernatchez
2019 Trends in Ecology & Evolution  
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

Sha Joe Zhu, Jason A Hendry, Jacob Almagro-Garcia, Richard D. Pearson, Roberto Amato, Alistair Miles, Daniel J Weiss, Tim CD Lucas, Michele Nguyen, Peter W Gething, Dominic Kwiatkowski, Gil McVean (+1 others)
2019 eLife  
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

Rodrigo Galhardi Gasparini, Ligia Yukie Sassaki, Rogerio Saad-Hossne
2018 Clinical and Experimental Gastroenterology  
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

Sándor Spisák, Norbert Solymosi, Péter Ittzés, András Bodor, Dániel Kondor, Gábor Vattay, Barbara K. Barták, Ferenc Sipos, Orsolya Galamb, Zsolt Tulassay, Zoltán Szállási, Simon Rasmussen (+5 others)
2013 PLoS ONE  
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

John E. Pool, Russell B. Corbett-Detig, Ryuichi P. Sugino, Kristian A. Stevens, Charis M. Cardeno, Marc W. Crepeau, Pablo Duchen, J. J. Emerson, Perot Saelao, David J. Begun, Charles H. Langley, Harmit S. Malik
2012 PLoS Genetics  
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]

Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Djomnang Kounatse, Joan Sesing Lenz, Randy Longman, Amy Steadman, Christopher Mason, Mirella Salvatore, Manikkam Suthan, John R Lee (+2 others)
2021 biorxiv/medrxiv  
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]

BJARNI V. HALLDÓRSSON, DEREK AGUIAR, SORIN ISTRAIL
2010 Biocomputing 2011  
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]

Nedda F. Saremi, Megan A. Supple, Ashley Byrne, James A. Cahill, Luiz Lehmann Coutinho, Love Dalén, Henrique V. Figueiró, Warren E. Johnson, Heather J. Milne, Stephen J. O'Brien, Brendan O'Connell, David P. Onorato (+11 others)
2018 bioRxiv   pre-print
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

Manuel A Rivas, Mélissa Beaudoin, Agnes Gardet, Christine Stevens, Yashoda Sharma, Clarence K Zhang, Gabrielle Boucher, Stephan Ripke, David Ellinghaus, Noel Burtt, Tim Fennell, Andrew Kirby (+26 others)
2011 Nature Genetics  
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]

Simon G Trevino, Standwell C Nkhoma, Shalini Nair, Benjamin J Daniel, Karla Moncada, Stanley Khoswe, Rachel L Banda, Francois Nosten, Ian H Cheeseman
2017 bioRxiv   pre-print
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

Iñigo Olalde, Federico Sánchez-Quinto, Debayan Datta, Urko M. Marigorta, Charleston W. K. Chiang, Juan Antonio Rodríguez, Marcos Fernández-Callejo, Irene González, Magda Montfort, Laura Matas-Lalueza, Sergi Civit, Donata Luiselli (+7 others)
2014 Scientific Reports  
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

Eugene Gonzalez-Lopez, Yuka Kawasawa-Imamura, Lijun Zhang, Xuemei Huang, Walter A. Koltun, Matthew D. Coates, Kent E. Vrana, Bertram Müller-Myhsok
2019 PLoS ONE  
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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