Exome sequencing
Whole exome sequencing (WES) was performed at the Massachusetts Eye and
Ear Ocular Genomics Institute using Agilent SureSelect Human All Exon v6
with the Illumina HiSeq 2000, or at the Broad Institute of MIT and
Harvard using a TWIST Biosciences custom exome bait with the Illumina
Novaseq 6000. We used the Ocular Genomics Institute bioinformatics
pipeline (Consugar et al., 2015) for alignment and variant calling that
includes the Burrows-Wheeler aligner (Li et al., 2010), GATK
(https://gatk.broadinstitute.org/), GERP
(http://mendel.stanford.edu/SidowLab/downloads/gerp/), Exome Aggregation
Consortium (ExAC) (http://exac.broadinstitute.org ), SIFT
(http://sift.jcvi.org/), and PolyPhen-2
(http://genetics.bwh.harvard.edu/pph2/). A coverage depth cutoff of 10x
was applied. Heterozygous was defined as a fraction of a variant base
between 0.25–0.75 and homozygous was defined as above 0.75. Average
coverage was 105x for 99% of coding sequences.