Direct Sequencing Of Genomic DNA Research Articles

Exon 87 skipping of the COL7A1 gene in dominant dystrophic epidermolysis bullosa

Dystrophic epidermolysis bullosa (DEB) is a rare, inherited, blistering disorder resulting from mutations in the COL7A1 gene, which encodes the anchoring fibrils, type VII collagen. We herein describe a further Japanese girl diagnosed with dominant DEB (DDEB). She had blisters sporadically and erosions healed with mild scarring and milia on the knees and pretibial regions. Severe pruritus was present at this time. Direct nucleotide sequencing of genomic DNA disclosed a heterozygous same splice-site mutation c.6900G>A in the COL7A1, which causes in-frame exon 87 skipping. So far, five different COL7A1 mutations leading to exon 87 skipping have been identified in rare forms of DEB: four DDEB pruriginosa and one pretibial DDEB. Therefore, a recent study suggested that exon 87 skipping in COL7A1 was related to the phenotype of DDEB pruriginosa. When she was 18 years old, however, the blister formation and pruritus markedly decreased. Therefore, her clinical symptoms were consistent to very mild DDEB but not to DDEB pruriginosa. Taken together, in-frame exon 87 skipping through c.6900G>A mutation may account for the mild skin features, rather than DDEB pruriginosa, in the present case.

Five novel mutations of SRD5A2 found in eight Chinese patients with 46,XY disorders of sex development

Individuals with male karyotype (46,XY) affected by 5α-reductase type 2 deficiency, a rare autosomal recessive inherited disorder, can have an almost female phenotype or partially virilized external genitalia. Mutations in the steroid-5-α-reductase (SRD5A2) gene, leading to functional impairment of 5α-reductase type 2, are responsible for this disorder. Our present study analyzed SRD5A2 gene mutations in eight unrelated 46,XY Chinese patients with disorders of sex development. Direct sequencing of genomic DNA for SRD5A2 gene revealed the presence of one homozygous (p.Q6X) and seven compound heterozygous mutations (p.G203S/R227Q, p.L20P/R227Q, p.Q6X/p.A228V, p.C222Ffs232X/p.R246Q, p.W140X/F219Sfs278X, p.Q71X/L185Tfs192X and p.Q6X/p.N193S) in our patients. Among them, p.C222Ffs232X, p.A228V, p.Q71X, L185Tfs192X and p.W140X mutations have not been previously reported. These novel mutations may provide us new insights into the molecular mechanism of 5α-reductase type 2 deficiency. Seven out of eight patients had at least one variant in exon 4, and 8 of 12 (66.7%) mutations were located in exon 4. The expanded mutation database of the SRD5A2 gene should benefit patients in the diagnosis and treatment of this disease.

A novel WASP gene mutation in a Chinese boy with Wiskott–Aldrich syndrome

Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disorder characterized by thrombocytopenia, small platelets, eczema, increased susceptibility to infection, and immunodeficiency. Mutations of the Wiskott-Aldrich syndrome protein (WASP) gene are responsible for this severe congenital disease. In this study, we report on a 2-year-old Chinese boy who presented with classic clinical WAS manifestations. By direct sequencing of cDNA and genomic DNA of the patient, we identified a novel mutation: the first nucleotide in exon 8 (G) had been deleted (769delG). This mutation results in two kinds of aberrant mRNA with abnormal splicing and causes frameshift and a stop codon at amino acid 260. Western blotting demonstrated a 28-kDa truncated WAS protein. A maternal study revealed that his mother had a heterozygous genotype, but showed normal WASP expression.

Absence of hotspot mutations in exons 9 and 20 of the PIK3CA gene in human oral squamous cell carcinoma in the Greek population

Phosphatidylinositol-3 kinases (PI3K) are a group of heterodimeric lipid kinases that regulate many cellular processes. Recent studies have reported high frequencies of somatic hotspot mutations in the phosphatidylinositol-3 kinase catalytic alpha (PIK3CA) gene, which encodes for one of these kinases, in several human solid tumors, including oral squamous cell carcinoma (OSCC). The aim of this study was to determine the frequency of hotspot mutations in exons 9 and 20 of the PIK3CA gene in OSCC in the Greek population. Eighty-six formalin-fixed and paraffin-embedded primary tumor specimens were analyzed by direct genomic DNA sequencing. Chi-square was used for statistical analysis. No hotspot mutations were detected in any of the samples. Two intronic polymorphisms IVS8 and IVS9 were detected, mainly in patients with cancer of the buccal mucosa and lower gingival and alveolus respectively. PIK3CA hotspot mutations are unlikely to play a major role in the pathogenesis of OSCC in the Greek population.

Identification and functional characterization of isocitrate dehydrogenase 1 (IDH1) mutations in thyroid cancer

Mutations in the genes for isocitrate dehydrogenase 1 (IDH1) and isocitrate dehydrogenase 2 (IDH2) have been recently identified in glioblastoma. In the present study, we investigated IDH1 and IDH2 mutations in follicular thyroid cancer (FTC) and anaplastic thyroid cancer (ATC), with the latter, like glioblastoma, having a rapidly aggressive and lethal clinical course. By direct genomic DNA sequencing, we analyzed exon 4 of the IDH1 and IDH2 genes that harbored the mutation hot spots codon 132 and 172 of the two genes in glioblastoma, respectively, in 12 thyroid cancer cell lines, 20 FTC, and 18 ATC tumor samples. A novel homozygous G367A IDH1 mutation, resulting in a G123R amino acid change in codon 123, was identified in a case of ATC. A previously described IDH1 V71I mutation was found in a case of FTC and a case of ATC and no mutations were found in the cell lines. The overall prevalence of mutations was thus 1/20 (5%) in FTC and 2/18 (11%) in ATC. We did not find mutation in the IDH2 gene in these thyroid cancer cell lines and tumor samples. Sequence alignment analysis of 16 species revealed that the novel IDH1 G123R mutation was located in a highly conserved region, raising the possibility of a serious functional consequence as could also be predicted by the occurrence of a positively charged amino acid from this mutation. To test this, we created a G123R mutant by site-directed mutagenesis and demonstrated a decreased enzymatic activity of IDH1, similar to the expected reduction in the enzymatic activity of the previously described R132H IDH1 mutant measured as a control. Thus, functionally relevant IDH1 mutations can also occur in thyroid cancer, particularly ATC, suggesting a potential tumorigenic role of the IDH1 system that could represent a new therapeutic target for thyroid cancer.

JAK1 mutations are not frequent events in adult T‐ALL: a GRAALL study

Activating somatic mutations in Tyrosine Kinase (TK) genes are frequent events in haematological malignancies, when they can provide promising therapeutic targets (Loriaux et al, 2008; Scholl et al, 2008). Somatic mutations of JAK1, a Janus Kinase (JAK) family member which plays important roles in normal and neoplastic haematopoiesis, were reported in 2/94 adult de-novo acute myeloid leukaemia (AML) (Xiang et al, 2008). Flex et al (2008) reported JAK1 mutations in acute lymphoblastic leukaemia (ALL), particularly in adult T lineage cases, where the mutation rate was 8/38 (21%). Mutations were found within the SH2 (exon 10), Pseudo-Tyr-Kinase (exons 13 and 15) and the Tyr-Kinase (exon 18) domains of JAK1, with 6/8 mutations occurring in exons 15 and 18. The structural and functional consequences of these mutations was variable in molecular modelling and in-vitro assays (Flex et al, 2008). Mutated cases were suggested to be associated with older patients and a poor outcome (Flex et al, 2008), despite the fact that all JAK1 mutated cases also demonstrated NOTCH1 mutations, which are known to be of favourable prognosis (Breit et al, 2006; Asnafi et al, 2009). Jeong et al identified JAK1 mutations in exons 13 and 16 in 3 of 11 adult T-ALL, but did not study exons 15 and 18 (Jeong et al, 2008). We therefore assessed JAK1 in adults with T-ALL included in the French prospective multicentre Group for Research on Adult Acute Lymphoblastic Leukaemia (GRAALL) study (Huguet et al, 2009). We screened for all of these mutations by direct sequencing of genomic DNA at diagnosis in 108 cases. Overall, JAK1 mutations were found in only four cases (Table I). Two of these mutations were previously reported and the two new mutations were absent from complete remission samples. The frequency of JAK1 mutation was significantly lower than expected and notably no mutation was observed within the TK domain. Flex et al (2008) reported that patients with mutated JAK1 allele are relatively old, consistent with the lower prevalence of mutation in childhood T-ALL. The overall median age in the present series was 30·5 years, identical to the JAK1 mutated cases (median 30 years, range 26–33 years). All JAK1 mutations were associated with NOTCH1 mutations (3/4 with PEST domain mutations associated or not with HD mutation) but this was not statistically significant because 60% of GRAALL T-ALL cases have NOTCH1 mutations (Asnafi et al, 2009). Two of the JAK1 mutated cases expressed TLX1 and a third expressed TLX3, but once again this did not have statistical value because 10 TLX3+ and 19 TLX1+ cases included in this study were JAK1 germline. Regarding the prognostic value of JAK1 mutations, all 4 cases achieved complete remission and 3/4 were cortico- and chemo-sensitive and were alive in first complete remission (CR1) at 54, 28 and 8 months from diagnosis. One patient was chemo-resistant and underwent bone marrow transplant-allograft in CR1 but died off-therapy from infectious complication. These data are in contradiction to the two previous reports (Flex et al, 2008; Jeong et al, 2008), and suggest that JAK1 mutations are rare in adult T-ALL from the GRAALL study, occurring in only 3·7% of patients, nor do they appear to be associated with a particularly poor outcome. These results merit confirmation in order to determine whether these differences are simply due to statistical variations, small patient numbers or whether factors, such as ethnic group, impact on the incidence of JAK1 mutations in adult T-ALL. We thank all clinicians and biologists from the GRAALL group for providing data and material and Chantal Persiaux and Caroline Caudron for technical assistance. This work was supported by the Laurette Fugain Association.

Association of Uncoupling Protein-1 Haplotypes with Body Fat Area

‡These authors contributed equally to this work. Obesity is a major cause of morbidity and mortality and is associated with risks for type 2 diabetes mellitus, heart disease, metabolic syndrome, hypertension, stroke, and certain forms of cancer. The glutamate decarboxylase 2 (GAD2), insulin-induced gene 2 (INSIG2), ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), melanocortin 4 receptor (MC4R), fresh touring origination (FTO), and uncoupling protein-1 (UCP-1) genes have been investigated for their association with obesity. Since the A-3826G SNP in the UCP-1 (uncoupling protein-1) gene was first shown to be the key genetic determinant of obesity and body fat accumulation, many studies have been performed in various populations to measure the association of the G allele of this SNP with obesity phenotypes. The association of the A-3826G single nucleotide polymorphism (SNP) with obesity has been controversial, however, suggesting that one SNP does not sufficiently explain the effects of ge nomic variation on body fat accumulation. In this study, 9 SNPs were newly identified in the 5’-flanking region of the UCP-1 gene by direct sequencing of genomic DNA from 21 Korean subjects, and 6 haplotypes were obtained by SNP genotyping and haplotype reconstruction. According to our haplotype analysis, ht2 of the G allele of A-3826G, was signifi cantly associated with overall fat measures after age and body weight were adjusted. Ht6 of the A allele of A-3826G, was significantly linked to reduced fat accumulation. These re sults provide an explanation for the controversies that have been reported in many obesity association studies and suggest that haplotype associations between polymorphic loci and neighbor loci that harbor functional sequence variants can be exploited to identify diseasepredisposing alleles.

P53 Inactivation and Genomic Aberrations in Relation to Imatinib Resistance in Chronic Myeloid Leukemia.

Abstract 4256 BackgroundImatinib resistance in chronic myeloid leukemia (CML) patients is correlated with mutations in BCR-ABL tyrosine kinase domain in about half of the cases. Additional mechanisms related to imatinib resistance are under investigation. As TP53 gene is an important tumor suppressor that triggers apoptosis in response to DNA damage, its inactivation is responsible for chemotherapy resistance in cancer. Its role in cellular response to targeted biological treatment is currently unresolved. Inactivation of p53 by deletion and/or mutation in the TP53 gene is observed in CML patients during progression to accelerated phase (AP) and blast crisis (BC). It was suggested that BCR-ABL inhibition by imatinib induce the p53 response and therefore p53 inactivation may play role in resistance to targeted treatment (Wendel et al., 2006; Yamamoto et al., 2008). On the other hand, imatinib-induced p53 independent pro-apoptotic mechanism was described recently (Liu et al., 2009). AimWe investigated the relationship between imatinib resistance and abnormalities in the TP53 gene and additional genomic changes. MethodsRNA and genomic DNA were isolated from peripheral blood mononuclear cells of CML patients that either fail to achieve or lost the major cytogenetic response (MCyR). TP53 mutational status was examined using functional analysis of separated alleles in yeast (FASAY). In defined cases direct sequencing of genomic DNA was used. Genomic changes were detected by conventional metaphase cytogenetics and CGH microarrays 4×44K (Agilent). Copy number analyses were performed using MEV software. ResultsFASAY analysis to detect functional state of TP53 gene was performed in 16 imatinib-resistant CML patients and in one Ph+ B-ALL patient. Six of these patients were negative for BCR-ABL mutations. Four patients were examined at the time of blast crisis (two patients with myeloid BC and two patients with lymphoid BC). All examined patients carried functional TP53 gene. As FASAY is based on RNA analysis, it is not able to detect some mutations leading to nonsense-mediated RNA decay; therefore, in six patients without BCR-ABL mutation, direct sequencing of TP53 gene from genomic DNA was performed. Also by this approach no TP53 mutation was detected. Alterations of the p53 pathway were found in only 2 patients, both in lymphoid BC: one patient without BCR-ABL mutation had +8 and the deletion of TP53 locus accompanied by i(17p). Second patient with BCR-ABL mutation T315I carried heterozygous deletion of 9p with biallelic loss of 9p21. In this locus two important tumor suppressor genes CDKN2A and CDKN2B are localized. CDKN2A alternative transcript contains an alternate open reading frame (ARF) that functions as a stabilizer of the tumor suppressor protein p53. In other two patients in chronic phase that did not reach MCyR and had no BCR-ABL mutations additional genomic changes potentially connected to imatinib resistance were found: 1) +der(16) coupled with amplification of 16(p11-q12), where ABCC11 and ABCC12 genes are localized. The proteins encoded by these genes are members of the superfamily of ATP-binding cassette (ABC) transporters responsible for multidrug resistance. 2) del(3)(p13p21), involving locus 3p14 where multiple tumor suppressors are localized (e.g. FHIT, ADAMTS9, LRIG1). Chromosomal region 3p14 was shown to be often deleted in different types of human cancers. ConclusionsImatinib resistance in CML patients is probably not associated with TP53 inactivation. Alterations of the p53 pathway occur within transformation to more advanced stages, what is in concordance with previous findings. Genomic aberrations potentially influencing response to imatinib treatment may be found in some patients. Larger patients' cohorts are required to identify relevant recurrent genomic aberrations involved in imatinib resistance.This work was supported with grants NR9858-4/2008 and NR9305-3/2007 provided by IGA MH CR of Czech Republic, and MSM0021622430 provided by MEYS of Czech Republic Disclosures:No relevant conflicts of interest to declare.

A novel deletion mutation is recurrent in von Willebrand disease types 1 and 3

Direct sequencing of VWF genomic DNA in 21 patients with type 3 von Willebrand disease (VWD) failed to reveal a causative homozygous or compound heterozygous VWF genotype in 5 cases. Subsequent analysis of VWF mRNA led to the discovery of a deletion (c.221-977_532 + 7059del [p.Asp75_Gly178del]) of VWF in 7 of 12 white type 3 VWD patients from 6 unrelated families. This deletion of VWF exons 4 and 5 was absent in 9 patients of Asian origin. We developed a genomic DNA-based assay for the deletion, which also revealed its presence in 2 of 34 type 1 VWD families, segregating with VWD in an autosomal dominant fashion. The deletion was associated with a specific VWF haplotype, indicating a possible founder origin. Expression studies indicated markedly decreased secretion and defective multimerization of the mutant VWF protein. Further studies have found the mutation in additional type 1 VWD patients and in a family expressing both type 3 and type 1 VWD. The c.221-977_532 + 7059del mutation represents a previously unreported cause of both types 1 and 3 VWD. Screening for this mutation in other type 1 and type 3 VWD patient populations is required to elucidate further its overall contribution to VWD arising from quantitative deficiencies of VWF.

Detection of combined genomic variants in a Jordanian family with familial non-autoimmune hyperthyroidism

Five patients, four brothers and their paternal aunt, presented with a history of overt hyperthyroidism and goiter. Hyperthyroidism in this family was remarkable for its poor response to carbimazole (30-50 mg/d). The thyroid ultrasound showed a diffusely enlarged gland in all the affected members, and thyroid stimulating antibodies (TSAB) were negative. Screening for germline mutations in thyroid stimulating hormone (TSH) receptor (TSHR) gene was performed by direct sequencing of genomic DNA extracted from peripheral blood leukocytes of all family members. The sequence analysis of all TSHR gene exons and intron borders revealed two genomic variants. The first was a single nucleotide polymorphism (SNP) within exon seven (Asn187Asn), whereas the other was located in intron seven (IVS7+68TG). All affected members, two asymptomatic brothers with sub-clinical hyperthyroidism, and their father were heterozygous for those two genomic variants. Anti-thyroid drug treatment for several months successfully relieved symptoms in one subject, whereas the remaining patients required total thyroidectomy to control their disease. This is the first Jordanian family with familial non-autoimmune hyperthyroidism, with mutations affecting the TSHR gene.

Functional Characterization of Low-Prevalence Missense Polymorphisms in the UDP-Glucuronosyltransferase 1A9 Gene

The UDP-glucuronosyltransferase (UGT) 1A9 has been shown to play an important role in the detoxification of several carcinogens and clearance of anticancer and pain medications. The goal of the present study was to identify novel polymorphisms in UGT1A9 and characterize their effect on glucuronidation activity. The UGT1A9 gene was analyzed by direct sequencing of buccal cell genomic DNA from 90 healthy subjects. In addition to a previously identified single nucleotide polymorphism (SNP) at codon 33 resulting in an amino acid substitution (Met>Thr), two low-prevalence (<0.02) novel missense SNPs at codons 167 (Val>Ala) and 183 (Cys>Gly) were identified and are present in both white and African-American subjects. Glucuronidation activity assays using HEK293 cell lines overexpressing wild-type or variant UGT1A9 demonstrated that the UGT1A9(33Thr) and UGT1A9(183Gly) variants exhibited differential glucuronidation activities compared with wild-type UGT1A9, but this was substrate-dependent. The UGT1A9(167Ala) variant exhibited levels of activity similar to those of wild-type UGT1A9 for all substrates tested. Whereas the wild-type and UGT1A9(33Thr) and UGT1A9(167Ala) variants formed homodimers as determined by Western blot analysis of native polyacrylamide gels, the UGT1A9(183Gly) variant was incapable of homodimerization. These results suggest that several low-prevalence missense polymorphisms exist for UGT1A9 and that two of these (M33T and C183G) are functional. These results also suggest that although Cys183 is necessary for UGT1A9 homodimerization, the lack of capacity for UGT1A9 homodimerization is not sufficient to eliminate UGT1A9 activity.

Comparison of genetic polymorphisms of theNAT2gene between Korean and four other ethnic groups

N-acetyltransferase 2 (NAT2) is responsible for the acetylation of numerous drugs and in the transformation of aromatic and heterocyclinc amines into carcinogenic intermediates. Polymorphism of NAT2 may contribute to interindividual variability in such acetylation. The aim of this study was to determine the allele frequencies of polymorphisms of the NAT2 gene, analyse linkage disequilibrium (LD) block and haplotypes in Koreans and compare them with those of other ethnic groups. We analysed genetic polymorphisms in all functional promoter and exons of the NAT2 gene by direct sequencing of genomic DNA from 192 healthy Korean subjects. The LD and haplotype blocks of these subjects were constructed from genotype data using an expectation-maximization algorithm. We compared these allele frequencies, LD block and haplotype structure with those of other ethnic groups registered on the International HapMap database. We identified 33 polymorphisms including six novel single nucleotide polymorphisms, -10778T>C, -10777A>G, -10351A>G, -10199C>T and -10104G>T in promoter and 578C>T in exon2 (T193M) in the Korean subjects tested. All allele frequencies reported in the Koreans were similar to those of Asians except for one allele (rs4345600, -9306A>G), whereas African and European groups had different frequencies in exon2. The haplotype structure and LD block among the five groups also revealed significant differences. Ethnic differences in the NAT2 genotype frequencies may be one of the important factors explaining variability in cancer incidence and drug toxicity. Our observations could be useful in assessing the susceptibility of different populations to cancer and contribute to better predictions of the pharmacokinetics and pharmacodynamics of drugs that are metabolized by NAT2, in different populations.

Mutation ofFOXL2in Granulosa-Cell Tumors of the Ovary

Granulosa-cell tumors (GCTs) are the most common type of malignant ovarian sex cord-stromal tumor (SCST). The pathogenesis of these tumors is unknown. Moreover, their histopathological diagnosis can be challenging, and there is no curative treatment beyond surgery. We analyzed four adult-type GCTs using whole-transcriptome paired-end RNA sequencing. We identified putative GCT-specific mutations that were present in at least three of these samples but were absent from the transcriptomes of 11 epithelial ovarian tumors, published human genomes, and databases of single-nucleotide polymorphisms. We confirmed these variants by direct sequencing of complementary DNA and genomic DNA. We then analyzed additional tumors and matched normal genomic DNA, using a combination of direct sequencing, analyses of restriction-fragment-length polymorphisms, and TaqMan assays. All four index GCTs had a missense point mutation, 402C-->G (C134W), in FOXL2, a gene encoding a transcription factor known to be critical for granulosa-cell development. The FOXL2 mutation was present in 86 of 89 additional adult-type GCTs (97%), in 3 of 14 thecomas (21%), and in 1 of 10 juvenile-type GCTs (10%). The mutation was absent in 49 SCSTs of other types and in 329 unrelated ovarian or breast tumors. Whole-transcriptome sequencing of four GCTs identified a single, recurrent somatic mutation (402C-->G) in FOXL2 that was present in almost all morphologically identified adult-type GCTs. Mutant FOXL2 is a potential driver in the pathogenesis of adult-type GCTs.

Further evidence that mutations in FGD4/frabin cause Charcot-Marie-Tooth disease type 4H

Autosomal recessive demyelinating Charcot-Marie-Tooth neuropathy type 4H (CMT4H) manifests early onset, severe functional impairment, deforming scoliosis, and myelin outfoldings in the nerve biopsy. Mutations in the FGD4 gene encoding the Rho-GTPase guanine-nucleotide-exchange-factor frabin were reported in five families. To characterize a novel mutation in FGD4 and describe the related phenotype. A 20-year-old woman born of healthy consanguineous parents and affected with early-onset peroneal muscular atrophy underwent standard clinical, electrophysiologic, and pathologic (sural nerve biopsy) investigations. Mutational analysis of FGD4 was performed by direct sequencing of genomic DNA. Transcriptional analysis was done by reverse transcriptase PCR on leukocyte RNA. The proband disclosed a moderately severe, scarcely progressive CMT, markedly slowed nerve conduction velocities, and a demyelinating neuropathy characterized by prominent myelin outfoldings. Mutational analysis disclosed a c.1762-2a>g transition in the splice-acceptor site of intron 14, which was predicted to cause a truncated frabin (p.Tyr587fsX14). The report confirms genetic heterogeneity of FGD4, demonstrates that CMT4H has variable functional impairment, and suggests that frabin plays a crucial role during myelin formation.

The g.−762T&gt;C polymorphism of the NPC1L1 gene is common in Chinese and contributes to a higher promoter activity and higher serum cholesterol levels

Niemann-Pick type C1-like 1 (NPC1L1) protein is responsible for intestinal cholesterol absorption. The aim of the study was to identify genetic polymorphisms of the NPC1L1 gene as well as their functional significance. The method involved screening of promoter and coding regions of the NPC1L1 gene for genetic polymorphisms by direct DNA sequencing of genomic DNA from 50 individuals. Functional studies on promoter polymorphisms were performed using luciferase assay. Association between the polymorphisms and serum cholesterol levels were investigated in 224 individuals. The results showed that in total, 11 single nucleotide polymorphisms were identified. Among them, a promoter polymorphism, g.-762T>C, and a synonymous polymorphism, g.1679C>G, were common (34 and 36%, respectively). These two polymorphisms were highly linked (D' value=0.7459, P-value <0.00001). For the g.-762T>C promoter polymorphism, luciferase assay in HepG2 cell line demonstrated that the -762C allele had a significantly higher promoter activity than the -762T allele (1.30+/-0.22 vs 0.37+/-0.06, 3.5-fold, P<0.05). We also showed that the NPC1L1 promoter activity was downregulated by cholesterol content in both genotypes. When association studies were performed, we found that -762C allele was associated with significantly higher serum total cholesterol and LDL-cholesterol content levels in a recessive model (LDL-cholesterol value=131.2+/-8.1 vs 116.4+/-2.2 mg dl(-1); total cholesterol value=214.7+/-9.0 mg dl(-1) vs 196.9+/-2.6, P-value <0.05, n=224). In conclusion, the C allele at -762 position of the NPC1L1 gene was common in people of Chinese ethnicity. The -762C allele had a higher promoter activity and was associated with a higher serum total cholesterol and LDL-cholesterol level.

An idiopathic epilepsy syndrome linked to 3q13.3‐q21 and missense mutations in the extracellular calcium sensing receptor gene

To identify the disease locus in a three-generation south Indian family having several of its members affected with idiopathic epilepsy. Genome-wide parametric linkage analysis was performed with 382 autosomal markers. Mutational analysis of the positional candidate genes in linked interval was performed by direct sequencing of genomic DNA from the proband in the family. Expression analysis in human adult brain was performed by Western blotting. A novel epilepsy genetic locus on chromosome 3q13.3-q21 was identified by linkage analysis. This locus comprises about 12 megabases of the genomic interval, with its proximal and distal genetic boundaries defined by microsatellite markers, D3S3675 and D3S1551, respectively. In this interval, we found a novel, patient-specific, missense variant, Arg898Gln, at the extracellular calcium sensing receptor (CASR), a gene belonging to the G-protein-coupled receptor family. CASR expression was detected in the temporal lobe, frontal lobe, parietal lobe, cerebellum, and hippocampus. Four additional, potentially pathogenic, missense CASR variants, Glu354Ala, Ile686Val, Ala988Val, and Ala988Gly, were observed in five individuals affected with idiopathic generalized epilepsy. A novel idiopathic epilepsy locus has been mapped on chromosome 3q13.3-q21, as evident by presence of significant genetic linkage. Identification of novel, rare missense CASR variants at evolutionary-conserved residues in epilepsy patients and CASR expression in various subregions of human brain raises an interesting possibility of involvement of CASR in pathophysiology of epileptic disorders.

Three NewBLMGene Mutations Associated with Bloom Syndrome

Bloom's syndrome (BS) is a rare autosomal recessive disease predisposing patients to all types of cancers affecting the general population. BS cells display a high level of genetic instability, including a 10-fold increase in the rate of sister chromatid exchanges, currently the only objective criterion for BS diagnosis. We have developed a method for screening the BLM gene for mutations based on direct genomic DNA sequencing. A questionnaire based on clinical information, cytogenetic features, and family history was addressed to physicians prescribing BS genetic screening, with the aim of confirming or guiding diagnosis. We report here four BLM gene mutations, three of which have not been described before. Three of the mutations are frameshift mutations, and the fourth is a nonsense mutation. All these mutations introduce a stop codon, and may therefore be considered to have deleterious biological effect. This approach should make it possible to identify new mutations and to correlate them with clinical information.

A novel mutation in hMLH1 gene in a Uruguayan Hereditary non-polyposis colorectal cancer (HNPCC-Lynch syndrome) family

22203 Background: HNPCC is the most common colorectal cancer syndrome and is associated with germ-line mutations in DNA mismatch repair genes (MMR). To date, more than 700 MMR gene mutations have been identified. The MMR gene mutation spectrum may vary across different populations and be influenced by founder mutations that prevail in specific ethnic groups. Uruguay is a small country without considerable genetic diversity and whose population is mainly originated from Southern Europe. We have previously reported an unexpectedly low frequency of molecularly defined HNPCC cases despite advanced methodology used for mutation detection, which may suggest the involvement of novel susceptibility genes. Methods: Ten Amsterdam positive families, seven of them without microsatellite instability (MSI) in their proband´s tumours, where thoroughly evaluated for mutations in hMLH1 and hMSH2 by Single-Strand Conformation Polymorphism (SSCP) and direct sequencing of genomic DNA from peripheral blood performed in the proband. Results: We identified a novel hMLH1 mutation (c.289T>G - Y97D) in a 37 year-old colorectal cancer patient from a family with eleven affected members, Amsterdam I positive criteria and without MSI. The affected family members are descendant of a Spanish family and the mean colon cancer diagnosis was 54 years old. This mutation has not been reported to the available databases (InSiGHT or the Newfoundland database). Conclusions: We identified a novel punctual germ-line mutation in hMLH1 in an HNPCC patient with microsatellite stable colorectal cancer. Absence of MSI in HNPCC patients is found only in 10–15% of cases. Southern Europe people represent mixed populations in which no particular mutation has been enriched and therefore it is not surprising that Uruguayan mutations differ from those found in Southern Europeans. However, novel mutations and the reported unexpectedly low frequency of molecularly defined HNPCC cases can be explained by a different mutational spectrum in the Uruguayan population which should be further investigated. No significant financial relationships to disclose.

Association of the T1799A BRAF mutation with tumor extrathyroidal invasion, higher peripheral platelet counts, and over-expression of platelet-derived growth factor-B in papillary thyroid cancer

The relationship among BRAF mutation, platelet counts, and platelet-derived growth factor (PDGF) with respect to clinicopathological outcomes of papillary thyroid cancer (PTC) may play a role in PTC pathogenesis but remains undefined. We examined the T1799A BRAF mutation by direct genomic DNA sequencing in 108 primary PTC samples from a Chinese cohort and analyzed its relationship with clinicopathological, hematological, and other laboratory results as well as the levels of expression of PDGF in tumors. We found that the BRAF mutation was significantly associated with extrathyroidal invasion and advanced tumor stages III and IV. Specifically, extrathyroidal invasion was seen in 30/54 (56%) PTC with BRAF mutation versus 18/54 (33%) PTC without the mutation (P=0.02). Tumor stages III and IV were seen in 16/54 (30%) PTC with BRAF mutation versus 7/54 (13%) PTC without the mutation (P=0.04). The BRAF mutation was also significantly associated with a higher platelet count, with 249.28+/-53.76 x 10(9)/l in the group of patients with BRAF mutation versus 207.79+/-58.98 x 10(9)/l in the group without the mutation (P=0.001). An association of higher platelet accounts with extrathyroidal invasion was also seen, with 242.66+/-51.85 x 10(9)/l in patients with extrathyroidal invasion versus 218.49+/-59.10 x 10(9)/l in patients without extrathyroidal invasion (P=0.03). The BRAF T1799A-positive PTC tissues harbored a significantly higher level of PDGF-B than BRAF T1799A-negative PTC tissues. The data suggest that the BRAF T1799A mutation is associated with aggressive pathological outcomes of PTC in which high platelet counts and increased PDGF production may play a role.

Mutation Detection Using Automated Fluorescence‐Based Sequencing

The development of high-throughput DNA sequencing techniques has made direct DNA sequencing of PCR-amplified genomic DNA a rapid and economical approach to the identification of polymorphisms that may play a role in disease. Point mutations as well as small insertions or deletions are readily identified by DNA sequencing. The mutations may be heterozygous (occurring in one allele while the other allele retains the normal sequence) or homozygous (occurring in both alleles). Sequencing alone cannot discriminate between true homozygosity and apparent homozygosity due to the loss of one allele due to a large deletion. In this unit, strategies are presented for using PCR amplification and automated fluorescence-based sequencing to identify sequence variation. The size of the project and laboratory preference and experience will dictate how the data is managed and which software tools are used for analysis. A high-throughput protocol is given that has been used to search for mutations in over 200 different genes at the Harvard Medical School - Partners Center for Genetics and Genomics (HPCGG, http://www.hpcgg.org/).