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.