Subject Population and Sample Collection
Recruitment of myelomeningocele subjects was in accordance with an institutional review board at the University of Texas Health Science Center at Houston and is described by Au et al . 2008 (Kit et al., 2008). The protocol for subject data collection was approved by the Committees for the Protection of Human Subjects at The University of Texas Medical School at Houston and Baylor College of Medicine.
We evaluated exome sequence data from both myelomeningocele and publicly available reference populations to look for genomic variation. Genomic DNA samples were used for exome capture with TargetSeq reagents (Life Technologies, Inc.) based on high density oligonucleotide hybridization of GENCODE annotated coding exons, NCBI CCDS, exon flanking sequences (including intron splice sites), small non-coding RNAs (e.g., microRNAs) and a selection of miRNA binding sites. After capture, libraries were constructed with addition of barcodes (AB Library Builder, Life Technologies, Inc.). Multiplexed sequencing used the Ion Proton platform (Life Technologies, Inc.) based on proton assays for polymerase sequencing of individual DNA molecules in wells of modified semiconductor chips.
Reference population variant data was retrieved from version 2 of the Genome Aggregation Database (gnomAD) (Karczewski et al., 2019). Specifically, we used gnomAD’s 8,556 “control” Admixed American (AMR) exome data that includes Mexican Americans, Puerto Ricans, Medellin Colombians, and Peruvians as well as gnomAD’s 21,384 “control” Non-Finnish European (NFE) exome data. The word “Hispanic” will be used when referring to both Mexican American cases and the AMR controls collectively. Likewise, the phrase “European ancestry” will be used when referring to both the European American cases and NFE controls together.