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Methods: Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array
- Hajime Matsuzaki,
- Halina Loi,
- Shoulian Dong,
- Ya-Yu Tsai,
- Joy Fang,
- Jane Law,
- Xiaojun Di,
- Wei-Min Liu,
- Geoffrey Yang,
- Guoying Liu,
- Jing Huang,
- Giulia C. Kennedy,
- Thomas B. Ryder,
- Gregory A. Marcus,
- P. Sean Walsh,
- Mark D. Shriver,
- Jennifer M. Puck,
- Keith W. Jones,
- and Rui Mei
Genome Res. March 2004 14: 414-425; doi:10.1101/gr.2014904
...errors in pedigree genotypes. PEDCHECK reports errors which include any inconsistencies between parents and offspring in nuclear families, as well as any male heterozygote calls in sex-linked chromosomes. A total of 38 family trios consisting of two parents and one child were genotyped. The families were...
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RESEARCH: Allele Frequency Distributions in Pooled DNA Samples: Applications to Mapping Complex Disease Genes
- Sarah H. Shaw,
- Minerva M. Carrasquillo,
- Carl Kashuk,
- Erik G. Puffenberger,
- and Aravinda Chakravarti
Genome Res. February 1, 1998 8: 111-123; doi:10.1101/gr.8.2.111
...the haplotype relative risk (HRR; Falk and Rubinstein 1987 ) test on parent–offspring trios. Consequently, we tested the accuracy of allele frequency estimates at 11 marker loci in a pool of 54 parental DNA samples and a pool of their 27 affected offspring. The samples were 27 trios in which each offspring...
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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...schematic, see Supplemental Fig. S9C,D), that combines calls from all three of these tools to genotype as many loci as possible while maintaining high call quality. Additionally, our trio experimental design provided a very low-level true signal of de novo mutations (discordant child–parent calls...
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Method: lobSTR: A short tandem repeat profiler for personal genomes
- Melissa Gymrek,
- David Golan,
- Saharon Rosset,
- and Yaniv Erlich
Genome Res. June 2012 22: 1154-1162; Published in Advance April 20, 2012, doi:10.1101/gr.135780.111
...(Ewen et al. 2000). With 53 coverage across all trio members, the MI rate was 95%; with 103 coverage, the MI rate was 97%; and with a coverage threshold of 15 or more, the MI rate was 99% (Fig. 4A). We also repeated the analysis only with discordant parental sites (for example, A/B call in one parent...
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Research: Alu repeat discovery and characterization within human genomes
- Fereydoun Hormozdiari,
- Can Alkan,
- Mario Ventura,
- Iman Hajirasouliha,
- Maika Malig,
- Faraz Hach,
- Deniz Yorukoglu,
- Phuong Dao,
- Marzieh Bakhshi,
- S. Cenk Sahinalp,
- and Evan E. Eichler
Genome Res. June 2011 21: 840-849; Published in Advance December 3, 2010, doi:10.1101/gr.115956.110
...and genotyping We focused on the parent–child trio (NA18506, NA18507, and NA18058) to assess the transmission characteristics of the novel Alu insertions. We performed two sets of experiments. First, we treated each individually and then compared the s for unique and shared Alu retrotransposons. We found...
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Resource: Maximum-likelihood estimation of recent shared ancestry (ERSA)
- Chad D. Huff,
- David J. Witherspoon,
- Tatum S. Simonson,
- Jinchuan Xing,
- W. Scott Watkins,
- Yuhua Zhang,
- Therese M. Tuohy,
- Deborah W. Neklason,
- Randall W. Burt,
- Stephen L. Guthery,
- Scott R. Woodward,
- and Lynn B. Jorde
Genome Res. May 2011 21: 768-774; Published in Advance February 8, 2011, doi:10.1101/gr.115972.110
...HapMap CEU parents from 30 parent–offspring trios and 25 HapMap TSI individuals) based on pairwise allele-sharing distances computed from ;247,000 SNPs typed on the Affymetrix SNP array (for additional details on data and methods, see Xing et al. 2010). The percentage of genetic variation explained...
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Research: Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis
- Brooke Weckselblatt,
- Karen E. Hermetz,
- and M. Katharine Rudd
Genome Res. July 2015 25: 937-947; Published in Advance June 12, 2015, doi:10.1101/gr.191247.115
...junctions had more than 4 bp of microhomology. To determine the parental origin of de novo translocations in EGL302 and EGL321, we genotyped family trios for heterozygous SNPs adjacent to chromosome breakpoints.We isolated SNPs from derivative chromosomes by sequencing junctions in the probands...
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Methods: Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies
- Kui Zhang,
- Zhaohui S. Qin,
- Jun S. Liu,
- Ting Chen,
- Michael S. Waterman,
- and Fengzhu Sun
Genome Res. May 2004 14: 908-916; Published in Advance April 12, 2004, doi:10.1101/gr.1837404
...haplotypes and untransmitted haplotypes from genotypes of the parents–offspring trios at each SNP independently. When the genotypes of the father, mother, and offspring at a locus are all available, we can uniquely infer the transmitted allele and untransmitted allele except when they have the same...
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RESEARCH: The Relative Power of Family-Based and Case-Control Designs for Linkage Disequilibrium Studies of Complex Human Diseases I. DNA Pooling
- Neil Risch and
- Jun Teng
Genome Res. December 1, 1998 8: 1273-1288; doi:10.1101/gr.8.12.1273
..., only the parents require individual genotyping to derive the TDT statistic, whereas all the offspring can be pooled. This can potentially lead to considerable savings in genotyping, especially for multiplex sibships. The formulas and tables we derive should provide some guidance to investigators...
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REVIEW: Copy number variation: New insights in genome diversity
- Jennifer L. Freeman,
- George H. Perry,
- Lars Feuk,
- Richard Redon,
- Steven A. McCarroll,
- David M. Altshuler,
- Hiroyuki Aburatani,
- Keith W. Jones,
- Chris Tyler-Smith,
- Matthew E. Hurles,
- Nigel P. Carter,
- Stephen W. Scherer,
- and Charles Lee
Genome Res. August 2006 16: 949-961; Published in Advance June 29, 2006, doi:10.1101/gr.3677206
...30 parent–offspring trios. The third population sample is 45 unrelated Han Chinese from Beijing, China, and the fourth population sample consists of 44 unrelated Japanese from Tokyo, Japan. Phase I of the HapMap Project provided a SNP genotype at ∼5-kb resolution in each of these 269 samples studied...

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