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Method: Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance
- Christopher J. Yoon,
- Su Yeon Kim,
- Chang Hyun Nam,
- Junehawk Lee,
- Jung Woo Park,
- Jihyeob Mun,
- Seongyeol Park,
- Soyoung Lee,
- Boram Yi,
- Kyoung Il Min,
- Brian Wiley,
- Kelly L. Bolton,
- Jeong Ho Lee,
- Eunjoon Kim,
- Hee Jeong Yoo,
- Jong Kwan Jun,
- Ji Seon Choi,
- Malachi Griffith,
- Obi L. Griffith,
- and Young Seok Ju
Genome Res. November/December 2022 32: 2134-2144; Published in Advance December 6, 2022, doi:10.1101/gr.276794.122
...of their genomic compositions would be necessary to provide appropriate medical care for such individuals.However, detecting DNA contamination by family members is challenging because of their shared DNA sequence by inheritance. A few tools have been developed for the estimation of DNA contamination among...
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Resource: Mitochondrial DNA variation across 56,434 individuals in gnomAD
- Kristen M. Laricchia,
- Nicole J. Lake,
- Nicholas A. Watts,
- Megan Shand,
- Andrea Haessly,
- Laura Gauthier,
- David Benjamin,
- Eric Banks,
- Jose Soto,
- Kiran Garimella,
- James Emery,
- Genome Aggregation Database Consortium,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Grace Tiao,
- Monkol Lek,
- Vamsi K. Mootha,
- and Sarah E. Calvo
Genome Res. March 2022 32: 569-582; Published in Advance January 24, 2022, doi:10.1101/gr.276013.121
...that addresses three technical challenges: (1) detecting homoplasmic and heteroplasmic variants, present, respectively, in all or a fraction of mtDNA molecules; (2) circular mtDNA ; and (3) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...-throughput metagenomic whole- sequencing (thereafter short as metagenomic) data sets ushered in a new era for understanding the ecological and evolutionary traits of the unculturable majority of natural microbiomes. However, high-quality (HQ, defined as >90% single copy gene [SCG]-completeness with <5% contamination...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...out of 50,769) compared with the Universal Human Reference RNA (UHRR) Iso-Seq data set, which comprises full-length isoforms from 10 human cell lines derived from multiple tissues (Supplemental Fig. S4). The AS events newly disclosed by deep long-read sequencing (73% of all detected events, 31,544 out...
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Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
- Hang Dai and
- Yongtao Guan
Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
...on contributions of unmapped reads. Nubeam is also useful in analyzing 16S rRNA sequencing data, which is a more prevalent type of data set in metagenomics studies. In our analysis, Nubeam recapitulated the findings that natural microbiota in mouse gut are resilient under challenges, and Nubeam detected...
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Resource: Improved definition of the mouse transcriptome via targeted RNA sequencing
- Giovanni Bussotti,
- Tommaso Leonardi,
- Michael B. Clark,
- Tim R. Mercer,
- Joanna Crawford,
- Lorenzo Malquori,
- Cedric Notredame,
- Marcel E. Dinger,
- John S. Mattick,
- and Anton J. Enright
Genome Res. May 2016 26: 705-716; doi:10.1101/gr.199760.115
...preparation protocol does not reliably measure small RNA species (Ozsolak and Milos 2011), we removed all isoforms shorter than 200 nt (Supplemental Fig. S7A). DNA contamination is an important consideration when detecting transcripts from sequencing data. Even with DNase treatment, it is possible...
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Method: Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens
- Victor C. Mason,
- Gang Li,
- Kristofer M. Helgen,
- and William J. Murphy
Genome Res. October 2011 21: 1695-1704; Published in Advance August 31, 2011, doi:10.1101/gr.120196.111
...multiple divergent species (Summerer 2009). This problem is exacerbated for museum specimens, where DNA quality varies greatly between samples and contamination levels are often high (Millar et al. 2008). Generation of whole sequences for museum specimens, or even complete mitochondrial DNA (mt...
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Research: Rapid coastal spread of First Americans: Novel insights from South America's Southern Cone mitochondrial genomes
- Martin Bodner,
- Ugo A. Perego,
- Gabriela Huber,
- Liane Fendt,
- Alexander W. Röck,
- Bettina Zimmermann,
- Anna Olivieri,
- Alberto Gómez-Carballa,
- Hovirag Lancioni,
- Norman Angerhofer,
- Maria Cecilia Bobillo,
- Daniel Corach,
- Scott R. Woodward,
- Antonio Salas,
- Alessandro Achilli,
- Antonio Torroni,
- Hans-Jürgen Bandelt,
- and Walther Parson
Genome Res. May 2012 22: 811-820; Published in Advance February 14, 2012, doi:10.1101/gr.131722.111
...1g and D1jAlthough D1 is a major pan-American founder lineage, its phylogeny is still poorly resolved, mainly due to the paucity of high-quality full mtDNA sequence data. By screening the Sorenson Molecular Genealogy Foundation (SMGF, http://www.smgf.org) mtDNA control region (CR) database...
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Research: Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication
- Andrew J. Heidel,
- Hajara M. Lawal,
- Marius Felder,
- Christina Schilde,
- Nicholas R. Helps,
- Budi Tunggal,
- Francisco Rivero,
- Uwe John,
- Michael Schleicher,
- Ludwig Eichinger,
- Matthias Platzer,
- Angelika A. Noegel,
- Pauline Schaap,
- and Gernot Glöckner
Genome Res. November 2011 21: 1882-1891; Published in Advance July 14, 2011, doi:10.1101/gr.121137.111
...tropics, but can also live under arctic, alpine, and desert conditions (Swanson et al. 1999). A molecular phylogeny based on SSU rRNA and a-tubulin sequence data subdivides the social amoebas into four taxon groups, with DD residing in group 4 (Schaap et al. 2006). Groups 1–3 are characterized by forming...
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LETTER: mtDNA phylogeny and evolution of laboratory mouse strains
- Ana Goios,
- Luísa Pereira,
- Molly Bogue,
- Vincent Macaulay,
- and António Amorim
Genome Res. March 2007 17: 293-298; Published in Advance February 6, 2007, doi:10.1101/gr.5941007
...phylogenies remain unexplored. By a phylogenetic analysis of newly generated complete mitochondrial DNA sequence data in 16 strains, we show here that all common inbred strains descend from the same Mus musculus domesticus female wild ancestor, and suggest that they present a different mitochondrial...

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