Deletion Carriers Research Articles

Neuroanatomical phenotypes in a mouse model of the 22q11.2 microdeletion

Recurrent deletions at the 22q11.2 locus have been established as a strong genetic risk factor for the development of schizophrenia and cognitive dysfunction. Individuals with 22q11.2 deletions have a range of well-defined volumetric abnormalities in a number of critical brain structures. A mouse model of the 22q11.2 deletion (Df(16)A+/−) has previously been utilized to characterize disease-associated abnormalities on synaptic, cellular, neurocircuitry, and behavioral levels. We performed a high-resolution MRI analysis of mutant mice compared with wild-type (WT) littermates. Our analysis revealed a striking similarity in the specific volumetric changes of Df(16)A+/− mice compared with human 22q11.2 deletion carriers, including in cortico-cerebellar, cortico-striatal, and cortico-limbic circuits. In addition, higher resolution compared with neuroimaging in human subjects allowed detection of previously unknown subtle local differences. The cerebellar findings in Df(16)A+/− mice are particularly instructive as they are localized to specific areas within both the deep cerebellar nuclei and the cerebellar cortex. Our study indicates that the Df(16)A+/− mouse model recapitulates most of the hallmark neuroanatomical changes observed in 22q11.2 deletion carriers. Our findings will help guide the design and interpretation of additional complementary studies and thereby advance our understanding of the abnormal brain development underlying the emergence of 22q11.2 deletion-associated psychiatric and cognitive symptoms.

Detection of Hb H Disease Genotypes Common in Northern Thailand by Quantitative Real-Time Polymerase Chain Reaction and High Resolution Melting Analyses

We used quantitative real-time polymerase chain reaction (qPCR) and high resolution melting (HRM) analyses for the detection of the common α-thalassemia (α-thal) genotypes in 40 northern Thai Hb H (β4) patients. The α0-thal [– –SEA (Southeast Asian) deletion] was detected by a multiplex gap real-time PCR. To determine the α+-thal, three primer pairs were designed. The A-primer pair was used to amplify the 3' terminal DNA sequences of the HBA2 gene, and the B-primer pair amplified the 5' flanking region of the HBA1 gene. The C-primer pair amplified the 3' terminal DNA sequences of the HBA1 gene and was used as an internal control. The –α4.2 (leftward) and –α3.7 (rightward) deletions were determined by monitoring the absence of PCR product(s). The Hb H patients who had a negative PCR result for the A-primer pair but positive for the B- and C-primer pairs carried the –α4.2 deletion, while the –α3.7 deletion carriers were negative for the A- and B-primer pairs. In the case of Hb H with Hb Constant Spring (Hb CS, α142, Term→Gln; HBA2: c.427T>C), all primer pairs were positive, HRM analysis of the PCR product of the A-primer pair was introduced to analyze the Hb CS gene. It can distinguish clearly between normal and Hb CS genotypes. The applied methods for the determination of the α0- and α+-thal genotypes revealed the results to be as accurate as conventional gap-PCR and the direct DNA sequencing methods but resulted in a much simpler and faster procedure.

Germline deletions in the EPCAM gene as a cause of Lynch syndrome – literature review

Lynch syndrome (clinically referred to as HNPCC – Hereditary Non-Polyposis Colorectal Cancer) is a frequent, autosomal, dominantly-inherited cancer predisposition syndrome caused by various germline alterations that affect DNA mismatch repair genes, mainly MLH1 and MSH2. Patients inheriting this predisposition are susceptible to colorectal, endometrial and other extracolonic tumors. It has recently been shown that germline deletions of the last few exons of the EPCAM gene are involved in the etiology of Lynch syndrome. Such constitutional mutations lead to subsequent epigenetic silencing of a neighbouring gene, here, MSH2, causing Lynch syndrome. Thus, deletions of the last few exons of EPCAM constitute a distinct class of mutations associated with HNPCC. Worldwide, several investigators have reported families with EPCAM 3’end deletions. The risk of colorectal cancer in carriers of EPCAM deletions is comparable to situations when patients are MSH2 mutation carriers, and is associated with high expression levels of EPCAM in colorectal cancer stem cells. A lower risk of endometrial cancer was also reported. Until now the standard diagnostic tests for Lynch syndrome have contained analyses such as immunohistochemistry and tests for microsatellite instability of mismatch repair genes. The identification of EPCAM deletions or larger EPCAM-MSH2 deletions should be included in routine mutation screening, as this has implications for cancer predisposition.

The glutathione S-transferase T1 deletion is associated with susceptibility to multiple sclerosis

BackgroundMultiple sclerosis (MS) occurs as a result of interaction between genetic and environmental factors. Recent data support the view that oxidative damage is one of an early event in MS tissue injury. The safe elimination of reactive oxygen species and toxins via glutathione S-transferase (GST) pathways is required in order to protect cells against reactive oxygen-induced damage. The aim of our study was to analyze the possible association of GSTM1 and GSTT1 gene polymorphisms with the susceptibility and clinical parameters of MS, in 455 consecutive patients and 366 controls. MethodsA multiplex polymerase chain reaction (PCR) was used to detect the deletions in GSTM1 and GSTT1 genes. ResultsPatients with MS had significantly higher frequency of GSTT1 null genotype compared to controls (37.36% vs. 21.86%, respectively, p<0.0001, adjusted OR 2.13 (1.56–2.90)), as well as double deletions (15.38% vs. 10.38%, respectively, p<0.05). The carriers of GSTM1 deletion had significantly earlier onset of MS compared to the wild-type carriers (28.31±8.45 vs. 30.64±9.30years, respectively, p=0.03). ConclusionThis study suggests the potential pathogenic role of GSTT1 deletion on MS susceptibility. There are no similar data published so far, yet this study should be replicated in other populations.

EPCAM germline and somatic rearrangements in lynch syndrome: identification of a novel 3′EPCAM deletion

3'EPCAM (Epithelial Cell Adhesion Molecule) genomic rearrangements can be a cause of mismatch repair deficiency in rare Lynch syndrome families. 3'EPCAM deletions include the polyadenylation signal and might result in promoter hypermethylation of the centromeric MSH2 gene in cis. A somatic rearrangement in trans affecting MSH2 is responsible for the final mismatch repair deficiency in the corresponding tumors but the mechanisms are not well documented. In this report two germline 3'EPCAM deletions are described together with the corresponding somatic mutations in the patient's colorectal tumors. Mutation and breakpoint analysis resulted in the identification of one novel (c.556-531_*872del) and one known EPCAM deletion (c.859-689_*14697del). Both deletions resulted from Alu mediated homologous recombination causing aberrant EPCAM-MSH2 fusion transcripts. The colorectal tumors of the deletion carriers were MSI-high. Strong hypermethylation of the MSH2 promoter was measured. Analysis of somatic genomic rearrangements showed a 4 Mb deletion including the EPCAM, MSH2 and MSH6 genes in one tumor and copy neutral loss of heterozygosity in the EPCAM-MSH2 region in the other tumor. This indicates that hemi- and homozygous hypermethylation of the MSH2 promoter and hence complete silencing of MSH2 expression was responsible for the mismatch repair deficiency in both colorectal tumors.

Studies on the molecular mechanisms of large deletion in the F8 gene in a severe haemophilia A patient

Objective To disclose the molecular mechanisms of large deletion in the F8 gene in a sever haemophilia A patient and to screen the potential carriers. Methods Coagulation assay was performed to establish the phenotype.LD-PCR and sequence-specific PCR were adopted for detecting intron 22 and intron 1 inversion of F8 gene.All the exons of F8 gene and its flanking sequences were amplified and sequenced directly.Deletion breakpoints were identified by primer walking strategy.Breakpoint-specific assays were performed for the identification of carriers.Multiplex fluorescent PCR was used to detect the polymorphism of six STR locus (F8Up226,F8Up146,F8Int13,F8Int25,F8Down48 and DXS1073) for gene linkage analysis. Results The proband had a significantly reduced activity of factorⅧ (<1%).Inversion of intron 22 and intron 1 showed negative results in the proband.Deletion of exons 4-7 in the F8 gene in the proband was suspected by the repeated failure to amplify the corresponding exons by PCR.Sequencing the products of prime walking showed that the patient had a deletion of 27 685 bp comprising exons 4-7,a 2-bp microhomology (AT) was observed at the breakpoint junction.The results of breakpoint-specific PCR showed that the fetal and the proband′s daughter were deletion carriers,consistent with the results of the genetic linkage analysis. Conclusions The deletion of exons 4-7 in the F8 gene results in a sever haemophilia A.Microhomology-mediated end-joining mediates the formation of detected deletion.The breakpoint-specific PCR provids a reliable diagnostic tool for identification of carrier status.(Chin J Lab Med,2013,36:534-537) Key words: Hemophilia A; Factor Ⅷ; Mutation; Exons; Multiplex polymerase chain reaction

Identification of a founder EPCAM deletion in Spanish Lynch syndrome families

Germline deletions at the 3'-end of EPCAM have been involved in the etiology of Lynch syndrome (LS). The aim of this study was to characterize at the molecular level Spanish families harboring EPCAM deletions. Non-commercial multiplex ligation-dependent probe amplification (MLPA) probes and long-range polymerase chain reaction (PCR) amplification were used to characterize each deletion. Haplotyping was performed by analyzing eight microsatellite markers and five MSH2single nucleotide polymorphisms (SNPs). Methylation of MSH2 was analyzed by methylation specific-MLPA. Tumors diagnosed in seven Spanish families harboring EPCAM deletions were almost exclusively colorectal. Mosaicism in MSH2 methylation was observed in EPCAM deletion carrier samples, being average methylation levels higher in normal colon and colorectal tumors (27.6% and 31.1%), than in lymphocytes and oral mucosa (1.1% and 0.7%). Three families shared the deletion c.858 + 2568_*4596del, with a common haplotype comprising 9.9 Mb. In two families the novel EPCAM deletion c.858 + 2488_*7469del was identified. This study provides knowledge on the clinical and molecular characteristics of mosaic MSH2 epimutations. The identification of an EPCAM founder mutation has useful implications for the molecular diagnosis of LS in Spain.

Abstract 3811: Rare variants at 16p11.2 and within TP53 influence neuroblastoma susceptibility.

Abstract Background: Neuroblastoma is a cancer of the sympathetic nervous system that most commonly affects young children and accounts for approximately 10% of all pediatric oncology deaths. We have reported common single nucleotide polymorphisms (SNPs) associated with neuroblastoma within LINC00340 (NEJM 2008), BARD1 (Nat Genet, 2009), LMO1 (Nature, 2010), DUSP12 and HSD17B12 (PLoS Genet, 2011), HACE1 and LIN28B (Nat Genet, 2012), and one common CNV at 1q21.1 within NBPF23 (Nature, 2009). Collectively, however, these variants still account for less than 10% of the risk for developing neuroblastoma. Based on this observation, along with the relative paucity of somatic mutations identified in this childhood cancer, we hypothesized that rare germline variants/mutations play a significant role in tumorigenesis. Methods and Results: We have taken a two-pronged approach to study both rare copy number variants (CNVs) and SNPs in neuroblastoma. First, we analyzed rare (&amp;lt; 1%) CNVs in a discovery cohort of 2,083 cases and 6,146 controls and identified several large (&amp;gt;500 Kb) CNVs associated with neuroblastoma, including a deletion at 16p11.2 (cases 0.43%, controls 0.04%; P = 4.0x10−4; OR: 8.9, 95% CI: 2.2-41.3). To date, we have replicated the 16p11.2 association in 1,167 neuroblastoma cases and 56,752 published controls (P=0.003; OR: 7.8, 95% CI: 2.3-23.6). In addition, we have validated by quantitative PCR several rare focal deletions of key developmentally regulated transcription factors, such as TBX2, detected in neuroblastoma patients but absent in 6,146 controls. In parallel, to identify relatively rare SNPs (0.5-5.0% minor allele frequency) influencing neuroblastoma susceptibility, we imputed genotypes using 1000 Genomes data in a discovery cohort of 2,101 neuroblastoma cases and 4,202 controls of European ancestry. We observed a strong association at rs78378222 (P = 6.4x10−9; OR: 2.1, 95% CI: 1.6-2.1) and rs35850753 (P = 2.2x10−9; OR: 1.9, 95% CI: 1.5-2.4), located in the 3' and 5' UTR of TP53 respectively. Both associations replicated robustly in our Italian and African-American case-series (combined rs78378222: P = 4.22 x 10−12, OR: 3.1, 95% CI: 2.1-10.1; rs35850753: P = 3.7 x 10−14; OR: 3.2, 95% CI: 2.0-9.7). These data add neuroblastoma to the subset of malignancies influenced by rs78378222, which disrupts the polyadenylation signal of TP53 having a hypomorphic effect and imparting cancer susceptibility (Nat Genet, 2011). Taken together, we show that rare CNVs and SNPs influence neuroblastoma susceptibility and have greater effect sizes than common variants reported thus far from GWAS. Efforts are ongoing to sequence the 16p11.2 region in deletion carriers and to understand the functional significance of the TP53 variants in neuroblastoma. Conclusions: Rare DNA variations at multiple loci have a significant influence on neuroblastoma tumorigenesis and begin to address the unexplained heritability of this cancer. Citation Format: Sharon J. Diskin, Mario Capasso, Maura Diamond, Kristopher Bosse, Hakon Hakonarson, Marcella Devoto, John M. Maris. Rare variants at 16p11.2 and within TP53 influence neuroblastoma susceptibility. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3811. doi:10.1158/1538-7445.AM2013-3811

ADRA2B genotype modulates effects of acute psychosocial stress on emotional memory retrieval in healthy young men

Previous studies have shown that acute psychosocial stress impairs retrieval of declarative memory with emotional material being especially sensitive to this effect. A functional deletion variant of the ADRA2B gene encoding the α2B-adrenergic receptor has been shown to increase emotional memory and neural activity in the amygdala. We investigated the effects of acute psychosocial stress and the ADRA2B allele on recognition memory for emotional and neutral faces. Fourty-two healthy, non-smoker male volunteers (30 deletion carriers, 12 noncarriers) were tested with a face recognition paradigm. During encoding they were presented with emotional and neutral faces. One hour later, participants underwent either a stress (“Trier Social Stress Test (TSST)”) or a control procedure which was followed immediately by the retrieval session where subjects had to indicate whether the presented face was old or new. Stress increased salivary cortisol concentrations, blood pressure and pulse and impaired recognition memory for faces independent of emotional valence and genotype. Participants showed generally slower reaction times to emotional faces. Carriers of the ADRA2B functional deletion variant showed an impaired recognition and slower retrieval of neutral faces under stress. Further, they were significantly slower in retrieving fearful faces in the control condition. The findings indicate that a genetic variation of the noradrenergic system may preserve emotional faces from stress-induced memory impairments seen for neutral faces and heighten reactivity to emotional stimuli under control conditions.

Homozygosity for a null allele of SMIM1 defines the Vel-negative blood group phenotype

The Vel antigen is present on red blood cells (RBCs) from all humans except rare Vel-negative individuals who can form antibodies to Vel in response to transfusion or pregnancy. These antibodies may cause severe hemolytic reactions in blood recipients. We combined SNP profiling and transcriptional network modeling to link the Vel-negative phenotype to SMIM1, located in a 97-kb haplotype block on chromosome 1p36. This gene encodes a previously undiscovered, evolutionarily conserved transmembrane protein expressed on RBCs. Notably, 35 of 35 Vel-negative individuals were homozygous for a frameshift deletion of 17 bp in exon 3. Functional studies using antibodies raised against SMIM1 peptides confirmed a null phenotype in RBC membranes, and SMIM1 overexpression induced Vel expression. Genotype screening estimated that ~1 of 17 Swedish blood donors is a heterozygous deletion carrier and ~1 of 1,200 is a homozygous deletion knockout and enabled identification of Vel-negative donors. Our results establish SMIM1 as a new erythroid gene and Vel as a new blood group system.

Identification of a novel in-frame deletion in KCNQ4 (DFNA2A) and evidence of multiple phenocopies of unknown origin in a family with ADSNHL

Autosomal dominant sensorineural hearing loss (ADSNHL) is extremely genetically heterogeneous, making it difficult to molecularly diagnose. We identified a multiplex (n=28 affected) family from the genetic isolate of Newfoundland, Canada with variable SNHL and used a targeted sequencing approach based on population-specific alleles in WFS1, TMPRSS3 and PCDH15; recurrent mutations in GJB2 and GJB6; and frequently mutated exons of KCNQ4, COCH and TECTA. We identified a novel, in-frame deletion (c.806_808delCCT: p.S269del) in the voltage-gated potassium channel KCNQ4 (DFNA2), which in silico modeling predicts to disrupt multimerization of KCNQ4 subunits. Surprisingly, 10/23 deaf relatives are non-carriers of p.S269del. Further molecular characterization of the DFNA2 locus in deletion carriers ruled out the possibility of a pathogenic mutation other than p.S269del at the DFNA2A/B locus and linkage analysis showed significant linkage to DFNA2 (maximum LOD=3.3). Further support of genetic heterogeneity in family 2071 was revealed by comparisons of audio profiles between p.S269del carriers and non-carriers suggesting additional and as yet unknown etiologies. We discuss the serious implications that genetic heterogeneity, in this case observed within a single family, has on molecular diagnostics and genetic counseling.

A significant effect of the TSPY1 copy number on spermatogenesis efficiency and the phenotypic expression of the gr/gr deletion

AZFc deletions cause a significant phenotypic heterogeneity with respect to spermatogenesis; however, the reason for this is poorly understood. Recently, testis-specific protein Y-encoded 1 (TSPY1) copy number variation (CNV) was determined to be a potential genetic modifier of spermatogenesis. We performed a large-scale cohort study to investigate the effect of TSPY1 CNV on spermatogenesis and to elucidate the possible contribution of TSPY1 genetic variation to the phenotypic expression of AZFc deletions. Haplogrouping of the Y-chromosome and quantification of the TSPY1 copy number were performed in 2272 Han Chinese males with different spermatogenic statuses (704 males with the b2/b4 or gr/gr deletion and 1568 non-AZFc-deleted males). Our data revealed that the TSPY1 copy number distributions were significantly different among non-AZFc-deleted males with different spermatogenic phenotypes. Lower sperm production and an elevated risk of spermatogenic failure were observed in males with fewer than 21 TSPY1 copies and in those with more than 55 copies relative to men with 21-35 copies. Similar results were observed in males with the gr/gr deletion. These findings indicate that TSPY1 CNV affects an individual's susceptibility to spermatogenic failure by modulating the efficiency of spermatogenesis and strongly suggest that there is a significant quantity effect of the TSPY1 copy number on the phenotypic expression of the gr/gr deletion. To our knowledge, this CNV is the first independent genetic factor that has been clearly observed to influence the spermatogenic status of gr/gr deletion carriers. A combined genetic analysis of the TSPY1 copy number and the gr/gr deletion could inform the clinical counselling of infertile couples.

MicroRNAs as the cause of schizophrenia in 22q11.2 deletion carriers, and possible implications for idiopathic disease: a mini-review

The 22q11.2 deletion is the strongest known genetic risk factor for schizophrenia. Research has implicated microRNA-mediated dysregulation in 22q11.2 deletion syndrome (22q11.2DS) schizophrenia-risk. Primary candidate genes are DGCR8 (DiGeorge syndrome critical region gene 8), which encodes a component of the microprocessor complex essential for microRNA biogenesis, and MIR185, which encodes microRNA 185. Mouse models of 22q11.2DS have demonstrated alterations in brain microRNA biogenesis, and that DGCR8 haploinsufficiency may contribute to these alterations, e.g., via down-regulation of a specific microRNA subset. miR-185 was the top-scoring down-regulated microRNA in both the prefrontal cortex and the hippocampus, brain areas which are the key foci of schizophrenia research. This reduction in miR-185 expression contributed to dendritic and spine development deficits in hippocampal neurons. In addition, miR-185 has two validated targets (RhoA, Cdc42), both of which have been associated with altered expression levels in schizophrenia. These combined data support the involvement of miR-185 and its down-stream pathways in schizophrenia. This review summarizes evidence implicating microRNA-mediated dysregulation in schizophrenia in both 22q11.2DS-related and idiopathic cases.

Adrenergic Receptor Polymorphisms and Prevention of Ventricular Arrhythmias With Bucindolol in Patients With Chronic Heart Failure

β-blockers prevent cardiac arrhythmias in patients with chronic heart failure and reduced left ventricular ejection fraction, including ventricular tachycardia/ventricular fibrillation (VT/VF). We hypothesized that prevention of ventricular arrhythmias by the β-blocker/sympatholytic agent bucindolol is influenced by genetic variation in adrenergic receptors. From a substudy of the β-Blocker Evaluation of Survival Trial (n=1040), we identified those with the high functioning 389Arg versus the lower function 389Gly β(1) adrenergic receptor variant, and the loss of function α(2c)322-325 adrenergic receptor deletion versus the 322 to 325 wild-type (Wt)/deletion variant. VT/VF was recorded on case report forms as an adverse event. There were 493 Arg 389 β(1) receptor homozygotes (β(1)389 Arg/Arg) versus 547 Gly389 carriers and 207 α(2c)322-325 deletion carriers versus 833 homozygous Wts (α(2c)322-325 Wt/Wt). In all genotypes bucindolol was associated with a lower incidence of VT/VF (subhazard ratio, 0.42 [0.27-0.64]; P=0.00006). Bucindolol reduced VT/VF in β(1)389 Arg homozygotes (subhazard ratio, 0.26 [0.14-0.50]; P=0.00005) but not in β(1)389 Gly carriers (subhazard ratio, 0.60 [0.34-1.07]; P=0.09). For genotype combinations, the α(2c)322-325 polymorphism altered the VT/VF bucindolol response in β1389 Gly carriers, with α(2c) deletion genotypes associated with complete efficacy loss. A test of interaction was statistically significant (P=0.028) for the treatment group and a β(1)389/α(2c)322-325 three genotype construct, effectively identifying patients who exhibited enhanced response, no substantial response modification and loss of response. Bucindolol prevents VT/VF in subjects with heart failure and reduced left ventricular ejection fractions, and this effect is modulated by β(1)389 Arg/Gly and α(2c)322-325 Wt/deletion adrenergic receptor polymorphisms.

A pilot study on collective effects of 22q13.31 deletions on gray matter concentration in schizophrenia.

The association of copy number variation (CNV) with schizophrenia has been reported with evidence of increased frequency of both rare and large CNVs. Yet, little is known about the impact of CNVs in brain structure. In this pilot study, we explored collective effects of all CNVs in each cytogenetic band on the risk of schizophrenia and gray matter variation measured in structural magnetic resonance imaging. With 324 participants’ CNV profiles (151 schizophrenia patients and 173 healthy controls), we first extracted specific CNV features that differ between patients and controls using a two sample t-test, and then tested their associations with gray matter concentration using a linear regression model in a subset of 301 participants. Our data first provided evidence of population structure in CNV features where elevated rare CNV burden in schizophrenia patients was confounded by the levels associated with African American subjects. We considered this ethnic group difference in the following cytoband analyses. Deletions in one cytoband 22q13.31 were observed significantly (p<0.05) more in patients than controls from all samples after controlling ethnicity, and the deletion load was also significantly (p = 1.44×10−4) associated with reduced gray matter concentration of a brain network mainly comprised of the cingulate gyrus and insula. Since 80% deletion carriers were patients, patients with deletions also showed reduced gray matter concentration compared with patients without deletions (p = 3.36×10−4). Our findings indicate that regional CNVs at 22q13.31, no matter the size, may influence the risk of schizophrenia with a remarkably increased mutation rate and with reduced gray matter concentration in the peri-limbic cortex. This proof-of-concept study suggests that the CNVs occurring at some ‘hotspots’ may in fact cause biological downstream effects and larger studies are important for confirming our initial results.

Polymorphic APOBEC3 modulates chronic hepatitis B in Moroccan population

The cytidine deaminase apolipoprotein B mRNA editing catalytic subunit-3 (APOBEC3) induces G-to-A hypermutation in hepatitis B virus (HBV) genomes and operates as part of the innate antiviral immune system. We investigated the associations between the presence of APOBEC3 variants and HBV carriage in a case-control study in the Moroccan population. A polymorphic deletion affecting the APOBEC3B gene and the H186R variant of APOBEC3G were genotyped in 179 HBV chronic carriers and 216 healthy control subjects. In addition, to assess the overall impact of APOBEC3 deaminases on circulating HBV, we looked for hyperedited forms of the viral genome using the 3DPCR technique and analysed editing context. Data analysis showed that there was no significant difference in the frequencies of deleted APOBEC3B alleles (P = 0.261) or genotypes (P = 0.333) between patients with chronic hepatitis B and control subjects. By contrast, subjects bearing deleted genotype had a faster progression of liver disease than those with the insertion genotype (adjusted OR, 3.72; 95% CI, 0.38-36.12). The analysis of the APOBEC3G H186R polymorphism revealed that R/R genotype frequencies were not significantly different in HBV infected patients and in healthy subjects. 3DPCR was positive in 26 samples (14%) among 179. Amplified viral segments displayed monomorphic G>A transitions highly reminiscent of APOBEC3G activity. Most intriguingly, hemi/homozygous carriers of the APOBEC3B deletion had significantly lower virus loads than patients with the wild type (median 539 vs. 2213 IU/mL, P = 0.0023). This result suggests that genetic variations in APOBEC3 cytidine deaminases do not predispose to chronicity but may modulate the course of persistent HBV infection.

EPCAM deletion carriers constitute a unique subgroup of Lynch syndrome patients

Lynch syndrome, one of the most common cancer susceptibility syndromes, is caused by germline mutations of genes affecting the mismatch repair proteins MLH1, MSH2, MSH6 or PMS2. Most of these mutations disrupt the open reading frame of the genes involved and, as such, lead to constitutive inactivation of the mutated allele. In a subset of Lynch syndrome patients MSH2 was found to be specifically inactivated in cell lineages exhibiting EPCAM expression. These patients carry deletions of the 3' end of the EPCAM gene, including its polyadenylation signal. Due to concomitant transcriptional read-through of EPCAM, the promoter of MSH2 15kb further downstream becomes inactivated through hypermethylation. As these 3' EPCAM deletions occur in the germline, this MSH2 promoter methylation ('epimutation') is heritable. Worldwide, numerous EPCAM 3' end deletions that differ in size and location have been detected. The risk of colorectal cancer in carriers of such EPCAM deletions is comparable to that of MSH2 mutation carriers, and is in accordance with a high expression of EPCAM in colorectal cancer stem cells. The risk of endometrial cancer in the entire group of EPCAM deletion carriers is significantly lower than that in MSH2 mutation carriers, but the actual risk appears to be dependent on the size and location of the EPCAM deletion. These observations may have important implications for the surveillance of EPCAM deletion carriers and, thus, calls for an in-depth assessment of clinically relevant genotype-phenotype correlations and its underlying molecular mechanism(s).

The modifier effect of the BDNF gene in the phenotype of the WAGRO syndrome

Individuals who are carriers of deletions of various sizes that cause haploinsufficiency in the contiguous WT1 and PAX6 genes, located on chromosome 11p13 approximately 4Mb centromeric to the BDNF gene, are susceptible to Wilms tumor, aniridia, mental retardation, genitourinary anomalies and obesity (WAGRO syndrome). The molecular characterization of the wide deletion 11p15.1p12 arr (18676926–36576388) x1 dn in a child with 3years and 4months of age only affected by aniridia, predicts not only other serious associated diseases, but also allows us to hypothesize a specific phenotype of mental impairment, conduct alterations and childhood obesity, possibly added to the onset of metabolic alterations. The variable appearance and/or description of haploinsufficiency for obesity susceptibility in the WAGR syndrome mainly depends on the critical region located within 80kb of exon 1 of BDNF. The relationship between genetic variation based on the genotype combinations of the 4 gene SNPs tagging the BDNF gene and the body mass index (BMI) was studied. The polymorphic variability was similarly distributed in 218 children suffering a severe and non-syndromic obesity from families at high risk for obesity, as compared with 198 controls. The corroborated role of the BDNF gene as highly susceptible to severe syndromic obesity has not already been evidenced in the molecular basis of overweight attributed to the common polygenic principles. Its potential role as risk modifier variant to provoke more severe phenotype has not yet been demonstrated. Some genetic variants of brain-derived neurotrophic factor (BDNF) have resulted in important disorders of energy balance, but it is essential to know exactly their deleterious human capacity because they play a fundamental role in the development and plasticity of the central nervous system in regulating food intake. The existence of polymorphic amino acid changes of unknown functional significance in patients carrying the haploinsufficiency of the BDNF gene could constitute an adequate model to study in depth their effects.

HNF1B deletions in patients with young-onset diabetes but no known renal disease.

Hepatocyte nuclear factor 1β (HNF1B) mutations cause a syndrome of renal cysts and diabetes, with whole gene deletions accounting for approximately 50% of cases. The severity of the renal phenotype is variable, from enlarged cystic kidneys incompatible with life to normal renal development and function. We investigated the prevalence of HNF1B deletions in patients with diabetes but no known renal disease. We tested 461 patients with familial diabetes diagnosed before 45 years, including 258 probands who met clinical criteria for maturity-onset diabetes of the young (two generations affected and at least one family member diagnosed under 25 years). A fluorescent polymerase chain reaction assay was used to analyse two intragenic polymorphic HNF1B markers and identify heterozygous patients who therefore did not have whole gene deletions. Those patients homozygous for both markers were then tested for an HNF1B deletion using multiplex ligation-dependent probe amplification. Heterozygous HNF1B intragenic polymorphisms were identified in 337/461 subjects. Multiplex ligation-dependent probe amplification analysis showed an HNF1B gene deletion in three of the remaining 124 probands, all of whom met the criteria for maturity-onset diabetes of the young. Testing of their relatives identified three additional deletion carriers and ultrasound scanning showed renal developmental abnormalities in three of these six patients. We estimate that HNF1B mutations account for < 1% of cases of maturity-onset diabetes of the young. Although HNF1B mutations are a rare cause of diabetes in the absence of known renal disease, a genetic diagnosis of renal cysts and diabetes syndrome is important as it raises the possibility of subclinical renal disease and the 50% risk of renal cysts and diabetes syndrome in the patient's offspring.

The Association of Angiotensin-Converting Enzyme Gene Insertion/Deletion Polymorphisms with Acute Mountain Sickness Susceptibility: A Meta-Analysis

Altitude exposure in nonacclimatized subjects may lead to acute mountain sickness (AMS). AMS is defined as headache upon recent arrival to altitude and may be accompanied by loss of appetite, nausea or vomiting, dizziness, fatigue, and poor sleep. Susceptibility for AMS varies and has been linked to angiotensin-converting enzyme (ACE) gene polymorphisms. We performed a meta-analysis of studies to assess the association between the ACE deletion (D) and insertion (I) alleles and AMS from published data. A fixed effects model was applied and study quality was assessed in duplicate. Five studies with a total of 333 AMS cases and 373 healthy controls were assessed. Our results revealed no significant differences in risk for AMS between carriers of ACE deletion and insertion polymorphism alleles.