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Chunk #2 — Methods and Materials — Autism Subphenotypes and Covariates

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Genome-wide linkage analyses of quantitative and categorical autism subphenotypes.
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The ADI ages of first words and phrases were specified in months for most individuals, but some individuals had been coded into groups. For example, code 993 was used for an individual who had some words then lost them. Due to the difficulties of imputing these “99x” codes into exact ages, these two variables were categorized into binary traits. Individuals who had delayed onset of first words (>24 months or the ADI-R code = 994 or 997) or first phrases (>36 months or the ADI-R code = 994 or 997) were coded as affected for the traits DelayedWord and DelayedPhrase, respectively. Table 1 in Supplement 1 lists the recoding of the 99x codes. Verbal/nonverbal status had three categories in the ADI-R—verbal, nonverbal with ≥5 words, and nonverbal with <5 words. The verbal category was treated as affected for the trait Verbal. Since different AGP sites used different instruments to measure IQ (though typically affected individuals from the same family would be tested with the same instrument), AGP required that each site provide the best estimate IQ in three categories, <50,