Antaki2021

A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex

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Data files

Data files include SummaryGeneticData_Reach_SSC_SPARK.csv and master_phen_4.csv (which includes clinical phenotype information). These will be deposited into SFARI.

Analysis code

The analysis code and code for generating figures are stored in the Colab notebooks.

Table of Contents

• SummaryGeneticData_Reach_SSC_SPARK

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Summary_Genetic_Data_REACH_SSC_SPARK

[SummaryGeneticData_Reach_SSC_SPARK]

This table contains the all the genetic features used for rare variant analysis, common variant analysis, and the construction of regression models.

Header

• FID
  • Family ID
• IID
  • Individual ID
• Phenotype
  • Phenotype: 1 = ASD; 0 = Control
• Sex
  • Sex: 0 = Male; 1 = Female
• Cohort
  • Data collection for a sample. Either REACH, SSC, or SPARK
• Family Type
  • Family structure for a given offspring. Either trio (both parents sequenced), maternal (mother only sequenced), or paternal (father only sequenced)
• Cases in Family
  • Number of affected children in a family. Simplex == 1
• EUR Ancestry
  • European Ancestry: 0 = False; 1 = True

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• dnMIS
  • Count of de novo missense SNV
• dnLoF
  • Count of de novo loss of function SNV/INDEL
• dnSV
  • Count of de novo LoF SVs

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• inhLoF

  • Count of inherited LoF SNV/INDEL

• inhLoF Paternal Transmitted

  • Count of paternally transmitted LoF SNV/INDEL

• inhLoF Paternal Untransmitted

  • Count of paternally nontransmitted LoF SNV/INDEL

• inhLoF Maternal Transmitted

  • Count of maternally transmitted LoF SNV/INDEL

• inhLoF Maternal Untransmitted

  • Count of maternally nontransmitted LoF SNV/INDEL

• SV LoF Paternal Transmitted

  • Count of paternally transmitted LoF SV

• SV LoF Paternal Untransmitted

  • Count of paternally nontransmitted LoF SV

• SV LoF Maternal Transmitted

  • Count of maternally transmitted LoF SV

• SV LoF Maternal Untransmitted

  • Count of maternally nontransmitted LoF SV

• CRE SV Paternal Transmitted

  • Count of paternally transmitted CRE SV

• CRE SV Paternal Untransmitted

  • Count of paternally nontransmitted CRE SV

• CRE SV Maternal Transmitted

  • Count of maternally transmitted CRE SV

• CRE SV Maternal Untransmitted

  • Count of maternally nontransmitted CRE SV

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• PS ASD

  • Autism polygenic risk score (PS) for the offspring

• PS ASD Father

  • Autism PS for the father

• PS ASD Mother

  • Autism PS for the mother

• Midparent PS ASD

  • Defined as (prs_asd_pat+prs_asd_mat)/2

• pTDT ASD Dev

  • Defined as prs_asd - midparent_prs_asd

• PS SCZ

  • Schizophrenia PS for the offspring

• PS SCZ Father

  • Schizophrenia PS for the father

• PS SCZ Mother

  • Schizophrenia PS for the mother

• Midparent PS SCZ

  • Defined as (prs_scz_pat+prs_scz_mat)/2

• pTDT SCZ Dev

  • Defined as prs_scz - midparent_scz_asd

• PS EA

  • Educational attainment PS for the offspring

• PS EA Father

  • Educational attainment PS for the father

• PS EA Mother

  • Educational attainment PS for the mother

• Midparent PS EA

  • Defined as (prs_ea_pat+prs_ea_mat)/2

• pTDT EA Dev

  • Defined as prs_ea - midparent_ea_asd

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• PC1 .. PC10
  • First ten ancestry principal components for the offspring
• PC1 Father .. PC2 Father
  • First two ancestry principal components for the father
• PC1 Mother .. PC2 Mother
  • First two ancestry principal components for the mother

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• RVRS
  • normalized estimates from multivariate regression combining de novo and inherited rare variants
• PRS
  • Normalized estimates from multivariate regression combining polygenic risk for autism, educational attainment, and schizophrenia
• GRS
  • Normalized estimates from multivariate regression combining de novo, inherited rare, and common variants

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