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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
...interpretation. Contamination would dilute true signals from the target (contaminated) DNA and introduce false signals from the source (contaminant) DNA, simultaneously generating false-negative and false-positive genotypes. Contamination of DNA can be caused by an experimental error in which samples...
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Method: Contamination detection in sequencing studies using the mitochondrial phylogeny
- Hansi Weissensteiner,
- Lukas Forer,
- Liane Fendt,
- Azin Kheirkhah,
- Antonio Salas,
- Florian Kronenberg,
- and Sebastian Schoenherr
Genome Res. February 2021 31: 309-316; Published in Advance January 15, 2021, doi:10.1101/gr.256545.119
...disease patients, also showing only moderate differences (mean, 107.2; SD, 36.4; DNA source, whole blood).Contamination detection in The 1000 Genomes Project ConsortiumTo evaluate haplocheck on a WGS study, we extracted the mtDNA reads (labeled as chromosome MT) from samples (Phase 3, low-coverage) from...
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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
...across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded contaminated samples, cell lines, and samples prone to NUMT misalignment due to few mtDNA copies...
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