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Introducing M-GCTA a software package to estimate maternal (or paternal) genetic effects on offspring phenotypes

Research output: Contribution to journalArticle

Original languageEnglish
Number of pages16
JournalBehavior Genetics
Early online date6 Sep 2019
DOIs
DateAccepted/In press - 27 Aug 2019
DateE-pub ahead of print (current) - 6 Sep 2019

Abstract

There is increasing interest within the genetics community in estimating the relative contribution of parental genetic effects on offspring phenotypes. Here we describe the user-friendly M-GCTA software package used to estimate the proportion of phenotypic variance explained by maternal (or alternatively paternal) and offspring genotypes on offspring phenotypes. The tool requires large studies where genome-wide genotype data are available on mother- (or alternatively father-) offspring pairs. The software includes several options for data cleaning and quality control, including the ability to detect and automatically remove cryptically related pairs of individuals. It also allows users to construct genetic relationship matrices indexing genetic similarity across the genome between parents and offspring, enabling the estimation of variance explained by maternal (or alternatively paternal) and offspring genetic effects. We evaluated the performance of the software using a range of data simulations and estimated the computing time and memory requirements. We demonstrate the use of M-GCTA on previously analyzed birth weight data from two large population based birth cohorts, the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Norwegian Mother and Child Cohort Study (MoBa). We show how genetic variation in birth weight is predominantly explained by fetal genetic rather than maternal genetic sources of variation.

    Research areas

  • SNP heritability, Heritability, G-REML, Paternal effects, Maternal effects, M-GCTA

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Documents

  • Full-text PDF (accepted author manuscript)

    Rights statement: This is the author accepted manuscript (AAM). The final published version (version of record) is available online via Springer Nature at https://link.springer.com/article/10.1007%2Fs10519-019-09969-4#enumeration. Please refer to any applicable terms of use of the publisher.

    Accepted author manuscript, 592 KB, PDF document

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  • Supplementary information PDF

    Accepted author manuscript, 395 KB, PDF document

    Embargo ends: 6/09/20

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