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Health and population effects of rare gene knockouts in adult humans with related parents

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Science  22 Apr 2016:
Vol. 352, Issue 6284, pp. 474-477
DOI: 10.1126/science.aac8624
  • Fig. 1 Discovery and annotation of rhLOF variants.

    (A) Autozygous segment numbers and length for UK-dwelling individuals of Pakistani heritage and European-heritage individuals from the 1000 Genomes Project (CEPH Utah residents with ancestry from Northern and Western Europe; CEU). (B) Autozygosity and rhLOF in 3222 individuals. The graph shows the number (count) of individuals (left y axis, blue columns) binned by fraction of the autozygous genome (F; x axis) plotted against the mean number of rhLOF genotypes per individual (right y axis, orange circles). (C) Distribution of LOF variants by variant type (allele frequency and heterozygous-only versus those containing a homozygous genotype), predicted protein consequence, and transcript completeness (i.e., whether predicted for a full or partial set of GENCODE basic transcripts for the gene).

  • Fig. 2 Population genetic analysis of rhLOF variants.

    (A) Comparison of the number of LOF variants per unit length in autozygous regions (LOF A) with the expected rate from nonautozygous sections (LOF NA), showing suppression of rhLOFs (t test). A similar analysis of synonymous (Syn) variants revealed no significant differences. (B) Observed number of variants with homozygote genotypes in 16,708 rare LOF variants (orange circle) versus a frequency-matched subsampling of synonymous variants (blue violin plot). (C) Quantification of the recessive lethal load carried, on average, by a single individual. Orange circle, direct subsampling estimate for rhLOF variants from current study; blue circles, epidemiological estimates from correlating infant mortality rates to estimated autozygosity in current and published data; green circle, direct estimate from a large Hutterite pedigree. Black bars denote 95% CIs. (D) Relative number of derived LOF alleles that are frequent in one population and not another (under neutrality, the expectation is 1.0). Results were calculated for 1000 Genomes Project populations and the current Birmingham/Bradford Pakistani heritage population (BB), as compared with the CEU population. Error bars represent ±1 (black) or 2 (gray) SEs. Significant differences (RA/B jackknife test) from CEU population data are denoted by orange circles. JPT, Japanese (Tokyo, Japan); BEB, Bengali (Bangladesh); TSI, Toscani (Italy); STU, Sri Lankan Tamil (UK); PJL, Punjabi (Lahore, Pakistan); CHB, Han Chinese (Beijing, China); ITU, Indian Telugu (UK); GIH, Gujarati Indian (Houston, TX); MSL, Mende (Sierra Leone); ESN, Esan (Nigeria); IBS, Iberian (Spain); LWK, Luhya (Webuye, Kenya); CDX, Chinese Dai (Xishuangbanna, China); YRI, Yoruba (Ibadan, Nigeria); GWD, Gambian (Western Divisions in the Gambia); GBR, British (England and Scotland); CHS, Southern Han Chinese (China); FIN, Finnish (Finland).

Supplementary Materials

  • Health and population effects of rare gene knockouts in adult humans with related parents

    Vagheesh M. Narasimhan, Karen A. Hunt, Dan Mason, Christopher L. Baker, Konrad J. Karczewski, Michael R. Barnes, Anthony H. Barnett, Chris Bates, Srikanth Bellary, Nicholas A. Bockett, Kristina Giorda, Christopher J. Griffiths, Harry Hemingway, Zhilong Jia, M. Ann Kelly, Hajrah A. Khawaja, Monkol Lek, Shane McCarthy, Rosie McEachan, Anne O'Donnell-Luria, Kenneth Paigen, Constantinos A. Parisinos, Eamonn Sheridan, Laura Southgate, Louise Tee, Mark Thomas, Yali Xue, Michael Schnall-Levin, Petko M. Petkov, Chris Tyler-Smith, Eamonn R. Maher, Richard C. Trembath, Daniel G. MacArthur, John Wright, Richard Durbin, David A. van Heel

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S8
    • Tables S1 to S8
    • Captions for Data S1 to S3
    • Full Reference List
    Data S1
    List of genes containing high confidence rhLOF genotypes, along with transcript specific annotation and numbers of heterozygote and homozygote genotypes in 3,222 individuals.
    Data S2
    Overlap of genes with homozygous LoFs across 3,222 British Pakistanis, 104,220 Icelanders, and 60,706 individuals in the ExAC dataset.
    Data S3
    Meiotic recombination crossover locations between mother and child for NA12878 duo as determined by pedigree and molecular phasing, along with crossover locations for PRDM9 duo.

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