High-throughput mutation detection method to scan BRCA1 and BRCA2 based on heteroduplex analysis by capillary array electrophoresis

8 páginas, 3 figuras, 2 tablas.[Background]: Scanning for mutations in BRCA1 and BRCA2 in a large number of samples is hampered by the large sizes of these genes and the scattering of mutations throughout their coding sequences. Automated capillary electrophoresis has been shown to be a powerful system to detect mutations by either single-strand conformation polymorphism or heteroduplex analysis (HA). [Methods]: We investigated the adaptation of gel-based HA of BRCA1 and BRCA2 to a fluorescent multicapillary platform to increase the throughput of this technique. We combined multiplex PCR, three different fluorescent labels, and HA in a 16-capillary DNA sequencer and tested 57 DNA sequence variants (11 insertions/deletions and 46 single-nucleotide changes) of BRCA1 and BRCA2. [Results]: We detected all 57 DNA changes in a blinded assay, and 2 additional single-nucleotide substitutions (1186 A>G of BRCA1 and 3624 A>G of BRCA2), previously unresolved by conformation-sensitive gel electrophoresis. Furthermore, different DNA changes in the same PCR fragment could be distinguished by their peak patterns. [Conclusions]: Capillary-based HA is a fast, efficient, and sensitive method that considerably reduces the amount of “hands-on” time for each sample. By this approach, the entire coding regions of BRCA1 and BRCA2 from two breast cancer patients can be scanned in a single run of 90 min.This work was supported by the Consejería de Sanidad (Junta y Castilla y León) through the regional Breast Cancer Prevention Program.Peer reviewe

Germline genetic findings which may impact therapeutic decisions in families with a presumed predisposition for hereditary breast and ovarian cancer

In this study, we aim to gain insight in the germline mutation spectrum of ATM, BARD1, BRIP1, ERCC4, PALB2, RAD51C and RAD51D in breast and ovarian cancer families from Spain. We have selected 180 index cases in whom a germline mutation in BRCA1 and BRCA2 was previously ruled out. The importance of disease-causing variants in these genes lies in the fact that they may have possible therapeutic implications according to clinical guidelines. All variants were assessed by combined annotation dependent depletion (CADD) for scoring their deleteriousness. In addition, we used the cancer genome interpreter to explore the implications of some variants in drug response. Finally, we compiled and evaluated the family history to assess whether carrying a pathogenic mutation was associated with age at diagnosis, tumour diversity of the pedigree and total number of cancer cases in the family. Eight unequivocal pathogenic mutations were found and another fourteen were prioritized as possible causal variants. Some of these molecular results could contribute to cancer diagnosis, treatment selection and prevention. We found a statistically significant association between tumour diversity in the family and carrying a variant with a high score predicting pathogenicity (p = 0.0003)

Twenty-three novel BRCA1 and BRCA2 sequence alterations in breast and/or ovarian cancer families of Eastern Spain

5 páginas, 1 tabla.-- et al.It is well established that mutations in BRCA1 and BRCA2 genes significantly increase the risk of breast and ovarian cancer. We here report 23 novel genetic variants of the BRCA1 and BRCA2 genes found in 349 cancer-prone unrelated families from Eastern Spain detected during the first 2 years of performance of the Program of Genetic Counseling of Valencia Community. Mutational screening was performed by pre-screening the heteroduplex formed in the PCR products obtained amplifying BRCA1 and BRCA2 genes by conformation sensitive electrophoresis. We detected 10 deletereous mutations, four in BRCA1 (three frame-shift (FS) and one nonsense mutation (NS)) and six in BRCA2 (four FS and one NS mutation). Moreover, we detected 13 unclassified variants, four in BRCA1 (one missense (MS), two synonymous (SYN) and one intronic (I) variant) and nine in BRCA2 (six MS, one SYN and two I). The relevance of the novel mutations is discussed. Our contribution broadens the BRCA1/2 world mutational spectra.Peer reviewe

High proportion of novel mutations ofBRCA1 andBRCA2 in breast/ovarian cancer patients from Castilla-León (central Spain)

7 páginas, 1 figura, 2 tablas.A total of 264 unrelated breast/ovarian cancer patients and 45 healthy individuals with familial antecedents referred for genetic testing were scanned for germ-line mutations in BRCA1 and BRCA2 by conformation-sensitive gel electrophoresis (CSGE) and heteroduplex analysis by capillary array electrophoresis (HA-CAE). We detected 101 distinct mutations (41 in BRCA1 and 60 in BRCA2); ten of them have not been previously reported. These mutations were c.2411_2429dup19, c.2802_2805delCAAA and c.5294A>G (p.E1725E) of BRCA1; and c.667C>T (p.Q147X), c.2683C>T (p.Q819X), c.5344_5347delAATA, c.5578_5579delAA;insT, c.8260_8261insGA, c.744+14C>T and c.8099A>G (p.Y2624C) of BRCA2. Twenty-four different mutations, including seven of the new mutations (five frameshift and two nonsense), were classified as pathogenic. These 24 alterations were found in 39 families (12.6% of all families). A remarkable proportion of deleterious mutations were found in BRCA2: 25 families carried a mutation in BRCA2 (BRCA2+; 64.1%) compared with 14 families BRCA1+ (35.9%). The highest incidences of deleterious mutations were found in families with three or more cases of site-specific breast cancer (BC) (27.4%) and families with BC and ovarian cancer (22.2%). Finally, four recurrent mutations, 3036_3039delACAA, c.5374_5377delTATG of BRCA2, as well as c.5272-1G>A and c.5242C>A (p.A1708E) of BRCA1, accounted for 44% of all of the deleterious mutations.This work has been supported by the Junta de Castilla y León through the regional Breast Cancer Prevention Program. M. Infante and E. Esteban-Cardeñosa were recipients of fellowships from the ‘‘Fundación Burgos para la Investigación en Salud.’’Peer reviewe

Genomic rearrangements at the BRCA1 locus in Spanish families with breast/ovarian cancer

6 páginas, 2 tablas.-- et al.[Background]: Large genomic rearrangements (LGRs) account for a substantial proportion of the BRCA1 disease-causing changes, or variations, identified in families with hereditary breast/ovarian cancer [HB(O)C]. Great differences in the spectrum and prevalence of BRCA1 LGR have been observed among populations. Here we report the first comprehensive analysis of BRCA1 LGRs conducted in Spain. [Methods]: We used multiplex ligation-dependent probe amplification (MLPA) to screen for BRCA1 LGRs in the index case individuals of 384 HB(O)C families who previously tested negative for BRCA1 and BRCA2 point variations, small insertions, and deletions. An alternative set of MLPA probes, long-range PCR, and real-time PCR were used to confirm positive results. [Results]: We have identified 8 different BRCA1 rearrangements (del exon 1–24, del exon 8–13, del exon 11–15, del exon 14, dup exon 19–20, dup exon 20, exon 21–22 amplification, and del exon 23–24). With the exception of del exon 8–13, they are novel alterations. Overall, BRCA1 LGRs explain 1.4% of the Spanish HB(O)C families, and they account for 8.2% of all BRCA1 pathogenic variations identified in our study population. BRCA1 genetic variants affecting hybridization of commercially available MLPA probes are very rare in our population. [Conclusions]: Screening for BRCA1 LGRs should be mandatory in Spanish HB(O)C families. A high proportion of country-specific rearrangements are scattered along the gene. MLPA is a robust method to screen for LGRs in our population. MLPA analysis of positive samples with an alternative set of probes, together with long-range PCR and real-time PCR, is a feasible approach to confirm results in cases in which LGR breakpoints have not been characterized.This work was supported by grants from Instituto de Salud Carlos III (FIS 01/3040, FIS 04/1832, FIS RTICC C03/10, and Xunta de Galicia (PGIDIT02PXIC20804PN). Sara Gutierrez-Enriquez is supported by a contract financed by Red Genómica del Cáncer del Instituto de Salud Carlos III (2003–2005).Peer reviewe

Mutational analysis of BRCA2 in Spanish breast cancer patients from Castilla-Leon: Identification of four novel truncating mutations

5 páginas, 2 tablas.Mutations in BRCA1 and BRCA2 account for approximately 5% of the overall familial risk of breast cancer. We have carried out a mutational analysis of the entire coding sequence of the BRCA2 gene in 150 breast cancer patients from Castilla-Leon by two different methods: Protein Truncation Test (PTT) and Conformation-Sensitive Gel Electrophoresis (CSGE). We have identified 10 distinct truncating mutations of the BRCA2 protein in 17 unrelated patients. Four mutations had not been previously described in any other population: two nonsense, Q2354X and K3083X, and two frameshift deletions, 6126delT and 5374delTATG. Moreover, three further mutations, 1538delAAGA, E1308X and S2219X, had not been reported in Spanish patients until now. Five mutations were recurrent: 3036delACAA, 1538delAAGA, 9538delAA and the novel mutations, 6126delT and 5374delTATG. The most prevalent mutation was 3036delACAA found in four unrelated patients.We thank the Junta de Castilla y León for its support.Peer reviewe

Detection by HRM and COLD-PCR-HRM BRAF mutational status in paraffin blocks of melanoma patients

Resumen del póster presentado a la European Human Genetics Conference celebrada en Nuremberg (Alemania) del 23 al 26 de junio de 2012.Over 50% of melanoma tumors have BRAF oncogene mutation. In 2011 we have obtained the first results of clinical trials of targeted therapy with molecules that act on BRAF signaling pathways (Ras/Raf/MEK/ERK). Vemurafenib and GSK2118436 showed an increase in overall survival and disease-free in p.V600E BRAF carriers patients. In the coming months, these molecules will be approved for clinical use in Europe. The application of analytical methods of high sensitivity in determining the mutational status of BRAF will be crucial to the imminent clinical application of new drugs, as the results will select patients eligible for or untreated. We have studied the 11 and 15 exons of BRAF by HRM.sequencing, and COLD-PCR-HRM-sequencing in 20 paraffin blocks of melanoma, previously studied by Sanger sequencing. Mutation was detected p.V600E of exon 15 in 9 of them for HRM, and 11 by COLD-HRM, compared to 8 previously detected by sequencing. The sensitivity of such methods as HRM and COLD-PCR-HRM is greater than sequencing. These results should be compared with those obtained by the propose clinical diagnostic tests (eg cobas 4800 BRAF V600 Mutation Test Roche©). Our previous results show the necessary standardization of the methods of detection of somatic mutations, especially in cases where the determined result to apply the therapy to the patient.Peer reviewe

The Average Cumulative Risks of Breast and Ovarian Cancer for Carriers of Mutations in BRCA1 and BRCA2 Attending Genetic Counseling Units in Spain

9 páginas, 1 figura, 4 tablas.-- et al.[Purpose]: It is not clear that the published estimates of the breast and ovarian cancer penetrances of mutations in BRCA1 and BRCA2 can be used in genetic counseling in countries such as Spain, where the incidence of breast cancer in the general population is considerably lower, the prevalence of BRCA2 mutations seems to be higher, and a distinct spectrum of recurrent mutations exists for both genes. We aimed to estimate these penetrances for women attending genetic counseling units in Spain. [Experimental Design]: We collected phenotype and genotype data on 155 BRCA1 and 164 BRCA2 mutation carrier families from 12 centers across the country. Average age-specific cumulative risks of breast cancer and ovarian cancer were estimated using a modified segregation analysis method. [Results]: The estimated average cumulative risk of breast cancer to age 70 years was estimated to be 52% [95% confidence interval (95% CI), 26-69%] for BRCA1 mutation carriers and 47% (95% CI, 29-60%) for BRCA2 mutation carriers. The corresponding estimates for ovarian cancer were 22% (95% CI, 0-40%) and 18% (95% CI, 0-35%), respectively. There was some evidence (two-sided P = 0.09) that 330A>G (R71G) in BRCA1 may have lower breast cancer penetrance. [Conclusions]: These results are consistent with those from a recent meta-analysis of practically all previous penetrance studies, suggesting that women with BRCA1 and BRCA2 mutations attending genetic counseling services in Spain have similar risks of breast and ovarian cancer to those published for other Caucasian populations. Carriers should be fully informed of their mutation- and age-specific risks to make appropriate decisions regarding prophylactic interventions such as oophorectomy.Peer reviewe

Detection of a large rearrangement in PALB2 in Spanish breast cancer families with male breast cancer

et al.It has been demonstrated that monoallelic PALB2 (Partner and Localizer of BRCA2) gene mutations predispose to familial breast cancer. Some of the families reported with germline PALB2 mutations presented male breast cancer as a characteristic clinical feature. Therefore, we wanted to investigate the contribution of germline PALB2 mutations in a set of 131 Spanish BRCA1/BRCA2-negative breast/ovarian cancer families with at least one male breast cancer case. The analysis included direct sequencing of all coding exons and intron/exon boundaries as well as a Multiplex Ligation-dependent Probe Amplification-based analysis of genomic rearrangements. For the first time we have identified a genomic rearrangement of PALB2 gene involving a large deletion from exon 7 to 11 in a breast cancer family. We have also identified several PALB2 variants, but no other obvious deleterious PALB2 mutation has been found. Thus, our study does not support an enrichment of PALB2 germline mutations in the subset of breast cancer families with male breast cancer cases. The identification of intronic and exonic variants indicates the necessity of assessing the implications of variants that do not lead to PALB2 truncation in the pathoghenicity of the PALB2 gene.This study was supported by grants from the Xunta de Galicia (10PXIB 9101297PR) and FMM Foundation given to AV. TC, M de H, and PPS were supported by PS09/00859, RD06/0020/0021 from RTICC, Instituto de Salud Carlos III. JB and AO were supports by the AECC, and RD06/0020/1060 from RTICC ICO: Contract grant sponsor: Asociación Española Contra el Cáncer, Spanish Health Research Fund; Carlos III Health Institute; Catalan Health Institute and Autonomous Government of Catalonia. Contract grant numbers: ISCIIIRETIC RD06/0020/1051, PI10/01422, PI10/ 31488, and 2009SGR290. E.V. grants, CSI004A10-2 (Consejería de Educación, Junta de Castilla y León) and BIO39/VA27/10 (Consejería de Sanidad, Junta de Castilla y León).Peer Reviewe

Molecular study of the BRCA1 and BRCA2 genes in 153 breast cancer families from Castilla y León (Spain): new nine unclassified variants identified

[ES]: Fundamento: El cáncer de mama hereditario representa un 5-10% de todos los cánceres de mama. En la actualidad dos genes están asociados a la enfermedad, el BRCA1 y el BRCA2. Se sabe que mutaciones en estos genes aumentan el riesgo de padecer cáncer de mama hasta en un 80% en las portadoras. El objetivo de este estudio es la detección y caracterización de mutaciones en estos genes, en pacientes con cáncer de mama seleccionadas según criterios de moderado-alto riesgo pertenecientes a la Comunidad Autónoma de Castilla y León. Pacientes y método: Se analizaron 207 muestras seleccionadas pertenecientes a 153 familias. Se realizó extracción de ADN de sangre periférica y para la detección de mutaciones se emplearon técnicas de PCR múltiplex-heterodúplex-CSGE y secuenciación. Resultados: Se detectaron 45 cambios nucleotídicos distintos (23 en BRCA1 y 22 en BRCA2) en 74 familias (48,4% del total), que corresponden a 13 polimorfismos (29 familias), 19 variantes de efecto desconocido (26 familias), de las que 9 son descritas por primera vez en este trabajo, y 13 patológicas (19 familias; 12,42% de las familias). De las mutaciones patológicas, 8 (42,1%) afectan a BRCA1 y 11 (57,9%) a BRCA2. La mutación más frecuente es la 3036delACAA de BRCA2, presente en 4 familias no relacionadas. Conclusiones: El alto porcentaje de mutaciones, polimorfismos y variantes de efecto desconocido detectado revela la alta resolución del método de análisis mutacional utilizado, así como la validez de los criterios de selección aplicados. Existe un gran número de variantes de significado desconocido cuyo papel en la enfermedad debe ser clarificado mediante diferentes tipos de estudios, entre los que se incluye su tipificación en poblaciones control.[EN]: Background: It is estimated that 5-10% of breast cancers have an hereditary origin, germline mutations of BRCA1 and BRCA2 genes causing a predisposition. In the present study we analyzed BRCA1 and BRCA2 mutations in moderate to high risk breast cancer patients in order to find out the types and frequency of these mutations in the Spanish regional community of Castilla y León. Patients and method: We studied 207 moderate to high risk patients from 153 selected families. Genomic DNA was extracted from peripheral blood and analyzed by multiplex polymerase chain reaction-heteroduplexes-conformation sensitive gel electrophoresis (multiplex PCR-HA-CSGE). All variants detected were sequenced to further verify the mutation. Results: 45 alterations (23 in BRCA1 and 22 in BRCA2) were identified in 74 families (48.4%), corresponding to 13 polymorphisms (29 families), 19 unclassified variants (26 families) ­of which 9 have not been previously described­ and 13 cancer-prone mutations (19 families; 12.42% of all families). Eight out of the 19 deleterious mutations (42.1%) were detected in the BRCA1 gene and 11 (57.9%) in the BRCA2 gene. The most prevalent mutation was 3036delACAA, which was detected in four unrelated families. Conclusions: The high proportion of mutations, polymorphisms and unclassified variants we have detected may be the result of the sensitive procedure and the risk selection criteria used in this study. There is a high proportion of unclassified variants. Their role in the disease must be clarified through more studies, including their typing in control samples.Peer reviewe