CFTR mutation analysis and haplotype associations in CF patients

Abstract

Most newborn screening (NBS) laboratories use second-tier molecular tests for cystic fibrosis (CF) using dried blood spots (DBS). The Centers for Disease Control and Prevention’s NBS Quality Assurance Program offers proficiency testing (PT) in DBS for CF transmembrane conductance regulator (CFTR) gene mutation detection. Extensive molecular characterization on 76 CF patients, family members or screen positive newborns was performed for quality assurance. The coding, regulatory regions and portions of all introns were sequenced and large insertions/deletions were characterized as well as two intronic di-nucleotide microsatellites. For CF patient samples, at least two mutations were identified/verified and four specimens contained three likely CF-associated mutations. Thirty-four sequence variations in 152 chromosomes were identified, five of which were not previously reported. Twenty-seven of these variants were used to predict haplotypes from the major haplotype block defined by HapMap data that spans the promoter through intron 19. Chromosomes containing the F508del (p.Phe508del), G542X (p.Gly542X) and N1303K (p.Asn1303Lys) mutations shared a common haplotype subgroup, consistent with a common ancient European founder. Understanding the haplotype background of CF-associated mutations in the U.S. population provides a framework for future phenotype/genotype studies and will assist in determining a likely cis/trans phase of the mutations without need for parent studies.

Deep resequencing of CFTR in 762 F508del homozygotes reveals clusters of non-coding variants associated with cystic fibrosis disease traits

“…Previously, a recombination event was reported to have occurred within intron 22. 25 However, this recombination event was based on population-level data provided by the HapMap project, which used wild-type CFTR and had significantly reduced marker density compared to this study. 48 Newer HapMap releases suggest two possible primary recombination events in the general population: intron 11 and intron 15-intron 16.…”

“…The intron 15 recombination event in F508del homozygotes is unique to this population, and is not apparent in HapMap populations (which contain a diversity of CFTR haplotypes only ~5% of which is the F508del ancestral haplotype), where a distinct recombination event within intron 22 is observed. 25 …”

Previously Unidentified Single Nucleotide Polymorphisms in HIV/AIDS Cases Associate with Clinical Parameters and Disease Progression

“…We observed the OAS2 T/C and C/C genotypes (rs2072137; chr12:113440921) to be associated with “typical” disease progression; however, the T/T genotype presented with higher frequency in the slow progressors. It is well documented that SNPs residing within introns, or those upstream or downstream of genes, also have the capacity to be causal [51–54]. In fact, in a recent study, Farh and colleagues utilized a fine-mapping algorithm to analyze GWAS data for 21 autoimmune diseases and reported that approximately 90% of all causal variants map to noncoding regions [55].…”

Synonymous SNPs of viral genes facilitate virus to escape host antiviral RNAi immunity

“…As reported, SNPs in the non-coding regions of a gene can manifest a higher risk of cancer (20) and can affect mRNA structure and disease susceptibility (21, 22). In the coding region, SNPs may result in a premature stop codon, a nonsense codon in the transcribed mRNA or in a truncated, incomplete and nonfunctional protein product (21). In recent years, it is found that synonymous SNPs are involved in codon usage preference or mRNA splicing (23-25).…”