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LASER server: ancestry tracing with genotypes or sequence reads

Daniel Taliun, Sonia P Chothani, Sebastian Schönherr, Lukas Forer, Michael Boehnke, Gonçalo R Abecasis, Chaolong Wang, Oliver Stegle
2017 Bioinformatics  
regardless of the sequencing strategy or genotyping array used to characterize each sample.  ...  To enable direct comparison of ancestry background in different studies, we developed LASER to estimate individual ancestry by placing either sezquenced or genotyped samples in a common ancestry space,  ...  Implementation The server is based on the LASER method, which can estimate ancestry using either genotypes or sequence reads (Supplementary Data).  ... 
doi:10.1093/bioinformatics/btx075 pmid:28200055 pmcid:PMC5870850 fatcat:trn37q3mijd77ihfsgx2vpftxa

Ancestry-agnostic estimation of DNA sample contamination from sequence reads [article]

Fan Zhang, Matthew Flickinger, InPSYght Psychiatric Genetics Consortium
2018 bioRxiv   pre-print
accurately estimates DNA contamination and is agnostic to genetic ancestry of the intended or contaminating sample.  ...  Correctly specifying population allele frequencies for each individual in early stage of sequence analysis is impractical or even impossible for large-scale sequencing centers that simultaneously process  ...  , with LASER and TRACE.  ... 
doi:10.1101/466268 fatcat:mcoam6i6jnhinmlb6n3mmeph7q

Large-scale whole-genome sequencing of three diverse Asian populations in Singapore [article]

Degang Wu, Jinzhuang Dou, Xiaoran Chai, Claire Bellis, Andreas Wilm, Chih Chuan Shih, Wendy Wei Jia Soon, Nicolas Bertin, Chiea Chuen Khor, Michael DeGiorgio, Sonia Maria Davila Dominguez, Patrick Tan (+12 others)
2018 bioRxiv   pre-print
Here we present whole-genome sequencing data of 4,810 Singaporeans from three diverse ethnic groups: 2,780 Chinese, 903 Malays, and 1,127 Indians.  ...  Finally, we demonstrate that our data can substantially improve genotype imputation not only for Singapore populations, but also for populations across Asia and Oceania.  ...  We inferred ancestry, sex, and contamination rate for each sample based on sequencing reads.  ... 
doi:10.1101/390070 fatcat:ag25it7nmrcgfdyfincgjbn7ei

Chromosome 1q21.2 and additional loci influence risk of spontaneous coronary artery dissection and myocardial infarction

Jacqueline Saw, Million Veteran Program, Min-Lee Yang, Mark Trinder, Catherine Tcheandjieu, Chang Xu, Andrew Starovoytov, Isabelle Birt, Michael R. Mathis, Kristina L. Hunker, Ellen M. Schmidt, Linda Jackson (+15 others)
2020 Nature Communications  
A polygenic risk score for SCAD was associated with (1) higher risk of SCAD in individuals with fibromuscular dysplasia (P = 0.021, OR = 1.82 [95% CI: 1.09-3.02]) and (2) lower risk of atherosclerotic  ...  × 10-6, OR = 0.96 [95% CI: 0.95-0.98] for MI).  ...  The association was tested using SAIGE with the same study design, which were age, sex, and ancestry (Locating Ancestry from SEquence Reads (LASER)/TRACE PCs) matched controls from the MGI samples, which  ... 
doi:10.1038/s41467-020-17558-x pmid:32887874 fatcat:cpwdekhhonf3xiej7utfq7ae7m

CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia

Kelly L. Williams, Simon Topp, Shu Yang, Bradley Smith, Jennifer A. Fifita, Sadaf T. Warraich, Katharine Y. Zhang, Natalie Farrawell, Caroline Vance, Xun Hu, Alessandra Chesi, Claire S. Leblond (+56 others)
2016 Nature Communications  
The mean read depth for these patients was  119.3, with an average of 6.01  10 9 base pairs sequenced per individual.  ...  exome variant server (6,503 sequenced human exomes), and ExAC database (40.001 frequency).  ... 
doi:10.1038/ncomms11253 pmid:27080313 pmcid:PMC4835537 fatcat:2lxsptjdsjc4te5rn4fsahpx7y

A genome-wide association analysis of loss of ambulation in dystrophinopathy patients suggests multiple candidate modifiers of disease severity [article]

Kevin M. Flanigan, Megan A. Waldrop, Paul T. Martin, Roxane Alles, Diane M. Dunn, Lindsay N. Alfano, Tabatha R. Simmons, Melissa Moore-Clingenpeel, John Burian, Sang-Cheol Seok, Robert B. Weiss, Veronica J. Vieland
2021 medRxiv   pre-print
the mRNA reading frame or allows expression of a partially functional protein.  ...  AbstractThe major determinant of disease severity in patients with severe Duchenne muscular dystrophy (DMD) or milder Becker muscular dystrophy (BMD) is whether their dystrophin gene (DMD) mutation disrupts  ...  The LASER/TRACE 2 server (https://laser.sph.umich.edu) was used to determine principal components from the genotype data, and for each study subject, we identified the 10 nearest reference individuals  ... 
doi:10.1101/2021.11.03.21265887 fatcat:ellgc2p7dbb6ha6h2rsqw6y7fq

A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

Neil A. Miller, Emily G. Farrow, Margaret Gibson, Laurel K. Willig, Greyson Twist, Byunggil Yoo, Tyler Marrs, Shane Corder, Lisa Krivohlavek, Adam Walter, Josh E. Petrikin, Carol J. Saunders (+9 others)
2015 Genome Medicine  
Here improvements in sequencing run time, read alignment, and variant calling are described that enable 26-h time to provisional molecular diagnosis with >99.5 % sensitivity and specificity of genotypes  ...  In such situations, delayed, empiric, or phenotype-based clinical decisions may meet with substantial morbidity or mortality.  ...  Comparison of the metrics of sequence yield and quality of 18-h and 26-h WGS (HiSeq 2500 2 × 100 nt rapid-run mode). a, R2 refers to read 2.  ... 
doi:10.1186/s13073-015-0221-8 pmid:26419432 pmcid:PMC4588251 fatcat:povwyqatyfampefkxxm3xrhk6y

Scalable Data Analysis of Mitochondrial DNA in the Era of High-Throughput Data Generation

Hansi Weissensteiner
2019 Figshare  
The developed tools help researchers working with mtDNA data on a daily base with in-depth quality control and are highly accepted by the community.  ...  This is especially true for mitochondrial DNA (mtDNA), which is used in a variety of disciplines, from archeogenetics, population- and forensic genetics or as well as clinical disease association studies  ...  This data is generated in high-throughput fashion by either reading the complete genome (e.g. sequencing with NGS) or by inspecting single positions on the DNA (e.g. genotyping with MicroArrays).  ... 
doi:10.6084/m9.figshare.8937899 fatcat:7g5oihrq2vekhb2d3apehiv4sm

DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gsα)-encoding (GNAS) genomic imprinting domain are associated with performance traits

Klaudia M Sikora, David A Magee, Erik W Berkowicz, Donagh P Berry, Dawn J Howard, Michael P Mullen, Ross D Evans, David E MacHugh, Charles Spillane
2011 BMC Genetics  
Results: SNP genotype-phenotype association analyses indicate that the single intronic GNAS SNP (rs41694646) is associated (P ≤ 0.05) with a range of performance traits including milk yield, milk protein  ...  The three remaining SNPs assayed were not associated with any of the performance traits analysed in this study.  ...  After data filtering, genotypic data for all six SNPs and 848 progeny-tested sires with an average co-ancestry of 2.2% remained.  ... 
doi:10.1186/1471-2156-12-4 pmid:21214909 pmcid:PMC3025900 fatcat:dllraridkjegfia4pb6lbytmu4

Genotyping ofMycobacterium tuberculosis: application in epidemiologic studies

Midori Kato-Maeda, John Z Metcalfe, Laura Flores
2011 Future Microbiology  
Genotyping is used to track specific isolates of Mycobacterium tuberculosis in a community.  ...  In this article, we review the genetic markers used in molecular epidemiologic studies including the use of whole-genome sequencing technology.  ...  with a different ancestry) and very rare homologous recombination events.  ... 
doi:10.2217/fmb.10.165 pmid:21366420 pmcid:PMC4296029 fatcat:yatajep3ofbi7e34c7xeny2sgi

Mutations in the unfolded protein response regulator ATF6 cause the cone dysfunction disorder achromatopsia

Susanne Kohl, Ditta Zobor, Wei-Chieh Chiang, Nicole Weisschuh, Jennifer Staller, Irene Gonzalez Menendez, Stanley Chang, Susanne C Beck, Marina Garcia Garrido, Vithiyanjali Sothilingam, Mathias W Seeliger, Franco Stanzial (+21 others)
2015 Nature Genetics  
Sequences were run on a capillary sequencer (ABI 3100, Applied Biosystems) and analyzed with Sequence Analysis software (version 5.1, Applied Biosystems) and sequence trace alignment software (SeqMan,  ...  The putative disease-causing variants were not observed in our in-house databases, dbSNP or the Exome Variant Server (EVS).  ...  (c) HEK293 cells were transfected with constructs for DHFR fused to YFP, wild-type ATF6A or Arg324Cys ATF6A, and trimethoprim (TMP) was added as indicated.  ... 
doi:10.1038/ng.3319 pmid:26029869 pmcid:PMC4610820 fatcat:rniivc5rdrdinj7hxe2xnqwwkm

A 48-plex Autosomal SNP GenPlex™ Assay for Human Individualization and Relationship Testing [chapter]

Carmen Tomas, Claus Børsting, Niels Morling
2011 Msphere  
except for brief excerpts in connection with reviews or scholarly analysis.  ...  Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden.  ...  Acknowledgments Many ICMP staff members have been involved in the development, validation, and/or long-term use of the protocols presented here; their excellent work and dedication is much appreciated.  ... 
doi:10.1007/978-1-61779-461-2_6 pmid:22139654 fatcat:ez7wcpvfzrdhnasrloc6rnuxza

Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm

Philippe Chetaille, Christoph Preuss, Silja Burkhard, Jean-Marc Côté, Christine Houde, Julie Castilloux, Jessica Piché, Natacha Gosset, Séverine Leclerc, Florian Wünnemann, Maryse Thibeault, Carmen Gagnon (+21 others)
2014 Nature Genetics  
Primer sequences are provided in Supplementary Table 4a . Sequencing traces were aligned to the genomic reference sequence using Lasergene SeqMan Pro software (DNASTAR). High-density genotyping.  ...  Variant positions were annotated with reference to Build 36 of the NCBI genome assembly and sequences NM_001199252 and NP_001186184. SGOL1 mutation genotyping.  ... 
doi:10.1038/ng.3113 pmid:25282101 fatcat:jbg3vy6jfvhhnapjxg2dy44fgm

Heterozygous Reelin Mutations Cause Autosomal-Dominant Lateral Temporal Epilepsy

Emanuela Dazzo, Manuela Fanciulli, Elena Serioli, Giovanni Minervini, Patrizia Pulitano, Simona Binelli, Carlo Di Bonaventura, Concetta Luisi, Elena Pasini, Salvatore Striano, Pasquale Striano, Giangennaro Coppola (+11 others)
2015 American Journal of Human Genetics  
We initially investigated 13 ADLTE-affected families by performing SNP-array linkage analysis and whole-exome sequencing and identified three heterozygous missense mutations co-segregating with the syndrome  ...  Homozygous RELN mutations are known to cause lissencephaly with cerebellar hypoplasia.  ...  Reads were aligned to the UCSC Genome Browser hg19 reference sequence with the Burrows-Wheeler Aligner, 14 and variant calling and genotyping were performed with the Genome Analysis Toolkit. 15 Variants  ... 
doi:10.1016/j.ajhg.2015.04.020 pmid:26046367 pmcid:PMC4457960 fatcat:v5aif2buundabbfiwot4mp2fz4

Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics

MichaelJ Becich, Lucas Santana-Santos, RamaR Gullapalli, KetakiV Desai, JeffreyA Kant
2012 Journal of Pathology Informatics  
Routine whole exome or even whole genome sequencing of clinical patients is well within the realm of affordability for many academic institutions across the country.  ...  This paper reviews current sequencing technology methods and upcoming advancements in sequencing technology as well as challenges associated with data generation, data manipulation and data storage.  ...  Most of the data generated from a bench-top sequencer can be easily analyzed with a high end desktop server.  ... 
doi:10.4103/2153-3539.103013 pmid:23248761 pmcid:PMC3519097 fatcat:qoxdhbrhtzbgvhxgpjl5jz2bym
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