Recombination as a mechanism for sporadic mutation in the surfactant protein-C gene

Abstract

Objective: To determine haplotype background of common mutations in the genes encoding surfactant proteins B and C (SFTPB and SFTPC) and to assess recombination in SFTPC.

Study design: Using comprehensive resequencing of SFTPC and SFTPB, we assessed linkage disequilibrium (LD) (D'), and computationally inferred haplotypes. We computed average recombination rates and Bayes factors (BFs) within SFTPC in a population cohort and near SFTPC (+/-50 kb) in HapMap cohorts. We then biochemically confirmed haplotypes in families with sporadic SFTPC mutations (n = 11) and in individuals with the common SFTPB mutation (121ins2, n = 30).

Results: We detected strong evidence (weak LD and BFs > 1,400) for an intragenic recombination hot spot in both genes. The 121ins2 SFTPB mutation occurred predominantly (89%) on 2 common haplotypes. In contrast, no consistent haplotypes were associated with mutated SFTPC alleles. Sporadic SFTPC mutations arose on the paternal allele in four of five families; the remaining child had evidence for somatic recombination on the mutated allele.

Conclusions: In contrast to SFTPB, disease alleles at SFTPC do not share a common haplotype background. Most sporadic mutations in SFTPC occurred on the paternal allele, but somatic recombination may be an important mechanism of mutation in SFTPC.

Copyright 2008 Wiley-Liss, Inc.

Figures

Figure. Detection of recombination hotspot in SFTPC

With examining recombination only within the 6 kb of SFTPC using the “population cohort” (filled symbols), the background recombination rate is markedly elevated (20-25 events/kb), making it difficult to detect a hotspot (low BF, 0.24 and 5.3, European (EA) and African (AA) descent, respectively). In contrast, with examining recombination across 100 kb surrounding and including SFTPC using HapMap data (open symbols), background recombination is still elevated (6-10 events/kb), but permits detection of markedly elevated values for the Bayes factor (1446 and 1416, European [CEU] and Yoruba [YRI], respectively) . For comparison, the genome wide average recombination rate is approximately 0.4 events / kb.