Initial exon sequencing of putatively acid-neutralizing basic proline rich proteins

Objectives: Susceptibility to dental caries might be detectable by genetic testing, but a suitable test has proved elusive. Dental caries is caused by dietary carboyhydrates inducing acid production within teeth-adherent bacterial biofilms. Adults with no caries neutralize these acids better than adults with severe caries, and their parotid saliva possesses longer, less fragmented basic proline rich proteins, BPRPs (Ayad et al. JDR 79:976, 2000). BPRPs bind to streptococcal adhesion antigen I/II (antigen c) where the longer BPRPs would neutralize acids better at sites of acid production. Because longer genes encode longer BPRPs, we investigated the possibility of exon sequencing BPRP alleles encoded by PRB1 and PRB2.  

Methods: All exons of PRB1 and PRB2 from 8 healthy adults were sequenced using an Illumina HiSeq 2000 (100 bp paired sequencing readouts with TruSeq™ Exome Enrichment Kit). Sequence reads were assembled to the human reference genome using Burrows-Wheeler Aligner software (BWA) and the Genome Analysis Tool Kit (GATK) which identifies genomic variants.

Results: Average read depth of these genes was approximately 100X. Nucleotide sequences contained numerous single nucleotide polymorphisms (SNPs), including amino acid to stop codon conversions and crossover events that deleted portions of PRB1 and/or PRB2. Of the 16 genes sequenced, 2 had a crossover between PRB1 and PRB2 and 4 had stop mutations. Unfortunately, precise genomic structure could not be determined with certainty due to high GC content and repetitive elements which negatively impacted read mapping accuracy.

Conclusions: Premature stop polymorphisms and partial deletions of PRB1 and/or PRB2 appear common in a European-American population and could partly explain the large variance in caries experience. High GC content difficulties can be addressed with available, improved sequencing chemistry, but difficulties in determining gene lengths may require complementary long read data (>500 bp) from the ROCHE platform with de novo assembly of each gene.