Quantification of sequence exchange events between PMS2 and PMS2CL provides a basis for improved mutation scanning of lynch syndrome patients

Heterozygous mutations in PMS2 are involved in Lynch syndrome, whereas biallelic mutations are found in Constitutional mismatch repair‐deficiency syndrome patients. Mutation detection is complicated by the occurrence of sequence exchange events between the duplicated regions of PMS2 and PMS2CL. We investigated the frequency of such events with a nonspecific polymerase chain reaction (PCR) strategy, coamplifying both PMS2 and PMS2CL sequences. This allowed us to score ratios between gene and pseudogene‐specific nucleotides at 29 PSV sites from exon 11 to the end of the gene. We found sequence transfer at all investigated PSVs from intron 12 to the 3′ end of the gene in 4 to 52% of DNA samples. Overall, sequence exchange between PMS2 and PMS2CL was observed in 69% (83/120) of individuals. We demonstrate that mutation scanning with PMS2‐specific PCR primers and MLPA probes, designed on PSVs, in the 3′ duplicated region is unreliable, and present an RNA‐based mutation detection strategy to improve reliability. Using this strategy, we found 19 different putative pathogenic PMS2 mutations. Four of these (21%) are lying in the region with frequent sequence transfer and are missed or called incorrectly as homozygous with several PSV‐based mutation detection methods. Hum Mutat 31:578–587, 2010. © 2010 Wiley‐Liss, Inc.     

Functional PMS2 hybrid alleles containing a pseudogene‐specific missense variant trace back to a single ancient intrachromosomal recombination event

Sequence exchange between PMS2 and its pseudogene PMS2CL, embedded in an inverted duplication on chromosome 7p22, has been reported to be an ongoing process that leads to functional PMS2 hybrid alleles containing PMS2‐ and PMS2CL‐specific sequence variants at the 5′‐and the 3′‐end, respectively. The frequency of PMS2 hybrid alleles, their biological significance, and the mechanisms underlying their formation are largely unknown. Here we show that overall hybrid alleles account for one‐third of 384 PMS2 alleles analyzed in individuals of different ethnic backgrounds. Depending on the population, 14–60% of hybrid alleles carry PMS2CL‐specific sequences in exons 13–15, the remainder only in exon 15. We show that exons 13–15 hybrid alleles, named H1 hybrid alleles, constitute different haplotypes but trace back to a single ancient intrachromosomal recombination event with crossover. Taking advantage of an ancestral sequence variant specific for all H1 alleles we developed a simple gDNA‐based polymerase chain reaction (PCR) assay that can be used to identify H1‐allele carriers with high sensitivity and specificity (100 and 99%, respectively). Because H1 hybrid alleles harbor missense variant p.N775S of so far unknown functional significance, we assessed the H1‐carrier frequency in 164 colorectal cancer patients. So far, we found no indication that the variant plays a major role with regard to cancer susceptibility. Hum Mutat 31:1–8, 2010. © 2010 Wiley‐Liss, Inc.     

A genetic variant in pseudogene E2F3P1 contributes to prognosis of hepatocellular carcinoma

Certain pseudogenes may regulate their protein-coding cousins by competing for miRNAs and play an active biological role in cancer. However, few studies have focused on the association of genetic variations in pseudogenes with cancer prognosis. We selected six potentially functional single nucleotide polymorphisms （SNPs） in cancerrelated pseudogenes, and performed a case-only study to assess the association between those SNPs and the prognosis of hepatocellular carcinoma （HCC） in 331 HBV-positive HCC patients without surgical treatment. Log-rank test and Cox proportional hazard models were used for survival analysis. We found that the A allele of rs9909601 in E2F3P1 was significantly associated with a better prognosis compared with the G allele [adjusted hazard ratio （HR） = 0.69, 95% confidence interval （CI） = 0.56-0.86, P = 0.001]. Additionally, this protective effect was more predominant for patients without chemotherapy and transcatheter hepatic arterial chemoembolization （TACE） treatment. Interestingly, we also detected a statistically significant multiplicative interaction between genotypes of rs9909601 and chemotherapy or TACE status on HCC survival （P for multiplicative interaction 〈 0.001）. These findings indicate that rs9909601 in the pseudogene E2F3P1 may be a genetic marker for HCC prognosis in Chinese.     

苯中毒与多聚二磷酸腺苷核糖聚合酶假基因多态等的相关性研究

目的探讨慢性苯中毒与微核率、姊妹染色单体互换(SCE)、多聚二磷酸腺苷核糖聚合酶(PARP)假基因多态的关系,为寻找苯中毒的易感者提供依据。方法对33例苯中毒病例与83例对照组进行微核率、SCE、PARP假基因多态的测定,并对其分布进行统计学分析。结果苯中毒病人外周血淋巴细胞微核率为0‰~6‰、中位数为2‰,对照组0‰~3‰,中位数为1‰;苯中毒病人SCE率为(6.31±1.26)次/细胞,对照组(5.59±0.18)次/细胞;苯中毒组与对照组微核率、SCE率差异有显著性(P<0.05);苯中毒组和对照组的PARP假基因中B基因频率分别为0.104和0.116,苯中毒组与对照组PARP假基因多态分布一致(P>0.05)。结论慢性苯中毒可引起微核率、SCE的增高,未发现PARP假基因多态与慢性苯中毒有关联。     

Germline BRCA1 promoter deletions in UK and Australian familial breast cancer patients: Identification of a novel deletion consistent with BRCA1:psiBRCA1 recombination

Inherited susceptibility to breast cancer results from germline mutations in one of a number of genes including BRCA1. A significant number of BRCA1-linked familial breast cancer patients, however, have no detectable BRCA1 mutation. This could be due in part to the inability of commonly used mutation-detection techniques to identify mutations outside the BRCA1 coding region. This paper addresses the hypothesis that non-coding region mutations, specifically in the BRCA1 promoter, account for some of these cases. We describe a new and detailed restriction map of the 5' region of the BRCA1 gene including the nearby NBR2, psiBRCA1, and NBR1 genes and the isolation of a number of new informative hybridization probes suitable for Southern analysis. Using this information we screened DNA from lymphoblastoid cell-lines made from 114 UK familial breast cancer patients and detected one large deletion in the 5' region of BRCA1. We show that the breakpoints for this deletion are in BRCA1 intron 2 and between NBR2 and exon 2 of psiBRCA1, raising the possibility that this deletion arose via a novel mechanism involving BRCA1:psiBRCA1 recombination. We have also screened 60 familial breast cancer patients from the Australian population, using an amplification refractory mutation system (ARMS) technique described previously by our group, and found one patient with a genotype consistent with a BRCA1 promoter deletion. These findings indicate that germline BRCA1 promoter deletions are a rare and yet significant mutation event and that they could arise via a novel genetic mechanism.     

应用双侧扩增阻滞突变系统排除肾上腺脑白质营养不良分子诊断中假基因的干扰

目的应用扩增阻滞突变系统（amplification refractory mutation system, ARMS）排除ABCD1假基因的干扰，对肾上腺脑白质营养不良（adrenoleukodystrophy，ALD）家系进行基因突变分析。方法按ARMS引物设计原则设计上游引物（正常引物、突变引物）和下游公共引物，对家系成员的基因组DNA分别进行PCR扩增。结果R617C突变患者及其母亲的突变引物均扩增出特异性条带（107bp），患者父亲和对照则未见条带，在基因组DNA水平证实了R617C突变的存在。结论双侧ARMS方法可以快速、有效地排除假基因干扰。     

相关基因多态性片段的研究

研究中国人RHD基因相关结构区的特征。采用PCR-SSP技术对随机非血缘关系RhD阳性样本100例,RhD阴性样本228例和Del样本42例的RHD基因的Rhesus盒、启动子区、第4内含子、ψ假基因、第9外显子1227G>A突变点研究。结果:存在RHD基因序列的样本(RHD~+/RHD~+,RHD~+/RHD)可测出启动子区3个多态性位点,有第4外显子者均有第4内含子,所有样本都检查不到RHDψ,34/42例Del样本可检测到1227G>A突变点。中国人RHD基因相关结构区有丰富的遗传背景,其生物学意义和遗传学意义有待进一步探讨。