Screening of CNVs using NGS data improves mutation detection yield and decreases costs in genetic testing for hereditary cancer.

INTRODUCTION: Germline CNVs are important contributors to hereditary cancer. In genetic diagnostics, multiplex ligation-dependent probe amplification (MLPA) is commonly used to identify them. However, MLPA is time-consuming and expensive if applied to many genes, hence many routine laboratories test only a subset of genes of interest. METHODS AND RESULTS: We evaluated a next-generation sequencing (NGS)-based CNV detection tool (DECoN) as first-tier screening to decrease costs and turnaround time and expand CNV analysis to all genes of clinical interest in our diagnostics routine. We used DECoN in a retrospective cohort of 1860 patients where a limited number of genes were previously analysed by MLPA, and in a prospective cohort of 2041 patients, without MLPA analysis. In the retrospective cohort, 6 new CNVs were identified and confirmed by MLPA. In the prospective cohort, 19 CNVs were identified and confirmed by MLPA, 8 of these would have been lost in our previous MLPA-restricted detection strategy. Also, the number of genes tested by MLPA across all samples decreased by 93.0% in the prospective cohort. CONCLUSION: Including an in silico germline NGS CNV detection tool improved our genetic diagnostics strategy in hereditary cancer, both increasing the number of CNVs detected and reducing turnaround time and costs.

Frecuencia y severidad de los síntomas en pacientes con Fibromialgia y Migraña / Frequency and severity of symptoms in patients with Fibromyalgia and Migraine

Objetivos: Estimar la frecuencia de migraña en pacientes con fibromialgia (FM). Describir y comparar características clínicas, socio demográficas y severidad de los síntomas de FM, según presencia o ausencia de migraña. Materiales y métodos: Estudio analítico, observacional, transversal. Incluyó pacientes mayores de 18 años, de ambos sexos con diagnóstico de FM según criterios ACR 2010 de un centro reumatológico público de Argentina entre enero de 2019 y marzo de 2020. Pacientes con otras enfermedades reumatológicas concomitantes fueron excluidos. Se utilizó criterios IHS (International Headache Society) para diagnóstico de migraña, FIQ (Fibromyalgia Impact Questionnaire) para evaluar severidad de los síntomas. Resultados: Se incluyeron 59 pacientes, 99% eran mujeres. El 40.68% de los pacientes presentaba migraña. En los pacientes con migraña, la mediana de puntaje del FIQ fue 70.35 (RIC: 63.16-78.76) vs 53.91 (RIC: 37.93-66.05) en el grupo sin migraña, siendo esta diferencia estadísticamente significativa (p<0.01). El análisis multivariado mostró al mayor puntaje del FIQ y de ansiedad, asociados de forma significativa e independiente con migraña (OR 1.048, IC 95%1.005-1.093); OR 1.189, IC 95%1.033-1.368, respectivamente. Conclusiones: La migraña es frecuente en pacientes con FM, y la severidad de los síntomas y la ansiedad serían más pronunciados en este grupo de pacientes.

Objectives: To estimate the frequency of migraine in patients with fibromyalgia (FM). Describe and compare clinical characteristics, sociodemographic and severity of FM symptoms, according to presence or absence of migraine. Materials and methods: Analytical, observational, cross-sectional study. It included patients over 18 years of age, of both sexes with a diagnosis of FM according to ACR 2010 criteria from a public rheumatology center in Argentina between January 2019 and March 2020. Patients with other concomitant rheumatological diseases were excluded. We used IHS (International Headache Society) criteria for the diagnosis of migraine, FIQ (Fibromyalgia Impact Questionnaire) were used to assess severity of symptoms. Results: 59 patients were included, 99% were women. 40.68% of the patients had migraine. In patients with migraine, the median FIQ score was 70.35 (IQR: 63.16-78.76) vs 53.91 (IQR: 37.93-66.05) in the group without migraine, this difference being statistically significant (p <0.01). The multivariate analysis showed a higher FIQ and anxiety score, significantly and independently associated with migraine (OR 1.048, 95% CI 1.005-1.093); OR 1,189, 95% CI 1,033-1,368, respectively). Conclusions: Migraine is frequent in patients with FM, and the severity of symptoms and anxiety would be more pronounced in this group of patients.

BARD1 Pathogenic Variants are Associated with Triple-Negative Breast Cancer in a Spanish Hereditary Breast and Ovarian Cancer Cohort.

Only a small fraction of hereditary breast and/or ovarian cancer (HBOC) cases are caused by germline variants in the high-penetrance breast cancer 1 and 2 genes (BRCA1 and BRCA2). BRCA1-associated ring domain 1 (BARD1), nuclear partner of BRCA1, has been suggested as a potential HBOC risk gene, although its prevalence and penetrance are variable according to populations and type of tumor. We aimed to investigate the prevalence of BARD1 truncating variants in a cohort of patients with clinical suspicion of HBOC. A comprehensive BARD1 screening by multigene panel analysis was performed in 4015 unrelated patients according to our regional guidelines for genetic testing in hereditary cancer. In addition, 51,202 Genome Aggregation Database (gnomAD) non-Finnish, non-cancer European individuals were used as a control population. In our patient cohort, we identified 19 patients with heterozygous BARD1 truncating variants (0.47%), whereas the frequency observed in the gnomAD controls was 0.12%. We found a statistically significant association of truncating BARD1 variants with overall risk (odds ratio (OR) = 3.78; CI = 2.10-6.48; p = 1.16 × 10-5). This association remained significant in the hereditary breast cancer (HBC) group (OR = 4.18; CI = 2.10-7.70; p = 5.45 × 10-5). Furthermore, deleterious BARD1 variants were enriched among triple-negative BC patients (OR = 5.40; CI = 1.77-18.15; p = 0.001) compared to other BC subtypes. Our results support the role of BARD1 as a moderate penetrance BC predisposing gene and highlight a stronger association with triple-negative tumors.

Comprehensive analysis and ACMG-based classification of CHEK2 variants in hereditary cancer patients.

CHEK2 variants are associated with intermediate breast cancer risk, among other cancers. We aimed to comprehensively describe CHEK2 variants in a Spanish hereditary cancer (HC) cohort and adjust the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) guidelines for their classification. First, three CHEK2 frequent variants were screened in a retrospective Hereditary Breast and Ovarian Cancer cohort of 516 patients. After, the whole CHEK2 coding region was analyzed by next-generation sequencing in 1848 prospective patients with HC suspicion. We refined ACMG-AMP criteria and applied different combined rules to classify CHEK2 variants and define risk alleles. We identified 10 CHEK2 null variants, 6 missense variants with discordant interpretation in ClinVar database, and 35 additional variants of unknown significance. Twelve variants were classified as (likely)-pathogenic; two can also be considered "established risk-alleles" and one as "likely risk-allele." The prevalence of (likely)-pathogenic variants in the HC cohort was 0.8% (1.3% in breast cancer patients and 1.0% in hereditary nonpolyposis colorectal cancer patients). Here, we provide ACMG adjustment guidelines to classify CHEK2 variants. We hope that this study would be useful for variant classification of other genes with low effect variants.

Comprehensive Constitutional Genetic and Epigenetic Characterization of Lynch-Like Individuals.

The causal mechanism for cancer predisposition in Lynch-like syndrome (LLS) remains unknown. Our aim was to elucidate the constitutional basis of mismatch repair (MMR) deficiency in LLS patients throughout a comprehensive (epi)genetic analysis. One hundred and fifteen LLS patients harboring MMR-deficient tumors and no germline MMR mutations were included. Mutational analysis of 26 colorectal cancer (CRC)-associated genes was performed. Pathogenicity of MMR variants was assessed by splicing and multifactorial likelihood analyses. Genome-wide methylome analysis was performed by the Infinium Human Methylation 450K Bead Chip. The multigene panel analysis revealed the presence of two MMR gene truncating mutations not previously found. Of a total of 15 additional MMR variants identified, five -present in 6 unrelated individuals- were reclassified as pathogenic. In addition, 13 predicted deleterious variants in other CRC-predisposing genes were found in 12 probands. Methylome analysis detected one constitutional MLH1 epimutation, but no additional differentially methylated regions were identified in LLS compared to LS patients or cancer-free individuals. In conclusion, the use of an ad-hoc designed gene panel combined with pathogenicity assessment of variants allowed the identification of deleterious MMR mutations as well as new LLS candidate causal genes. Constitutional epimutations in non-LS-associated genes are not responsible for LLS.

Exploring the Role of Mutations in Fanconi Anemia Genes in Hereditary Cancer Patients.

Fanconi anemia (FA) is caused by biallelic mutations in FA genes. Monoallelic mutations in five of these genes (BRCA1, BRCA2, PALB2, BRIP1 and RAD51C) increase the susceptibility to breast/ovarian cancer and are used in clinical diagnostics as bona-fide hereditary cancer genes. Increasing evidence suggests that monoallelic mutations in other FA genes could predispose to tumor development, especially breast cancer. The objective of this study is to assess the mutational spectrum of 14 additional FA genes (FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FANCP, FANCQ, FANCR and FANCU) in a cohort of hereditary cancer patients, to compare with local cancer-free controls as well as GnomAD. A total of 1021 hereditary cancer patients and 194 controls were analyzed using our next generation custom sequencing panel. We identified 35 pathogenic variants in eight genes. A significant association with the risk of breast cancer/breast and ovarian cancer was found for carriers of FANCA mutations (odds ratio (OR) = 3.14 95% confidence interval (CI) 1.4-6.17, p = 0.003). Two patients with early-onset cancer showed a pathogenic FA variant in addition to another germline mutation, suggesting a modifier role for FA variants. Our results encourage a comprehensive analysis of FA genes in larger studies to better assess their role in cancer risk.

Medical therapy using omeprazole in 12 hydrocephalic dogs: clinical, diagnostic, and therapeutic findings / Terapia médica utilizando omeprazol em 12 cães hidrocefálicos: achados clínicos, diagnósticos e terapêuticos

According to experimental studies with healthy dogs, omeprazole might decrease the CSF production by about 26%; therefore, book texts have been suggested the usage of omeprazole in medical protocols for hydrocephalus treatment. However, to the best knowledge of the authors, the usage and medical response of the omeprazole with substantial group of illness dogs, such as hydrocephalic animals, was lacking. This report describes clinical, diagnostic, and therapeutic findings in 12 dogs with hydrocephalus in which omeprazole were used for medical treatment. The diagnosis of hydrocephalus was accomplished by transcranial sonography (TCS) and/or computed tomography. The ventricular measurement was assessed periodically by TCS during medical treatment. Six dogs were diagnosed with non-obstrutive hydrocephalus and in the other 6 cases hydrocephalus occurred with other concomitant anomalous encephalic disease often related with obstructive hysdrocephalus, such as quadrigeminal cist, arachnoid cyst, chiary-like malformation, and syringomyelia. All of them had medical improvement after the use of omeprazole and the most of the cases had ventricular size reduction. In 10 dogs, the omeprazole was used as single drug, and in 2 dogs medical treatment with steroids and/or diuretics was previously being performed, and omeprazole was added because conventional treatment was resulting in mild to unsatisfactory medical control of the neurological status. The results of this paper shown that omeprazole may be used to ameliorate the neurological status in symptomatic hydrocephalic dogs. This work may represent the first description about the use of omeprazole in order to treat a substantial group of affected dogs with suspected increased intracranial pressure by hydrocephalus, probably due to limitation of CSF production.(AU)

O omeprazol diminui a produção do fluido cerebrospinal (FCE) por cerca de 26% de acordo com estudos experimentais em cães saudáveis. Segundo o conhecimento dos autores, embora utilizado na prática clínica e recomendado em livros textos, não há até o momento estudos clínicos em um grupo substancial de animais avaliando a resposta terapêutica ao uso do omeprazol em pacientes enfermos, tais como cães hidrocefálicos sintomáticos. Este trabalho descreve os achados clínicos, diagnósticos e terapêuticos em 12 cães com hidrocefalia que foram submetidos ao tratamento com omeprazol para o manejo médico de hidrocefalia. O diagnóstico de hidrocefalia e doenças neurológicas concomitantes foi realizado por ultrassonografia transcraniana (USTC) e/ou tomografia computadorizada. A mensuração do tamanho ventricular foi realizada pela USTC durante o tratamento médico. Seis cães foram diagnosticados com hidrocefalia não obstrutiva e os outros 6 casos apresentaram hidrofalia concomitante com outras afecções encefálicas anômalas comumente associada à hidrocefalia obstrutiva, tal como cisto quadrigêmio, cisto aracnóide, síndrome de chiari-like e seringomegalia. Em 10 cães o omeprazol foi utilizado como droga única e em 2 cães a terapia inicial foi a convencional utilizando esteroides e diuréticos, e o omeprazol foi adicionado, pois a resposta clínica a terapia convencional foi insatisfatória. Todos os animais obtiveram melhora dos parâmetros neurológicos e a maioria teve uma redução do tamanho ventricular após o uso do omeprazol. Os resultados deste estudo demonstram que o omeprazol pode ser utilizado para melhorar o estado neurológico em cães com hidrocefalia. Este estudo representa a primeira descrição clínica usando o omeprazol para tratar uma série de cães com suspeita de aumento da pressão intracraniana devido à hidrocefalia, provavelmente pela capacidade do fármaco em limitar a produção do FCE.(AU)

Does multilocus inherited neoplasia alleles syndrome have severe clinical expression?

IMPORTANCE: Genetic testing of hereditary cancer using comprehensive gene panels can identify patients with more than one pathogenic mutation in high and/or moderate-risk-associated cancer genes. This phenomenon is known as multilocus inherited neoplasia alleles syndrome (MINAS), which has been potentially linked to more severe clinical manifestations. OBJECTIVE: To determine the prevalence and clinical features of MINAS in a large cohort of adult patients with hereditary cancer homogeneously tested with the same gene panel. PATIENTS AND METHODS: A cohort of 1023 unrelated patients with suspicion of hereditary cancer was screened using a validated panel including up to 135 genes associated with hereditary cancer and phakomatoses. RESULTS: Thirteen (1.37%) patients harbouring two pathogenic mutations in dominant cancer-predisposing genes were identified, representing 5.7% (13/226) of patients with pathogenic mutations. Most (10/13) of these cases presented clinical manifestations associated with only one of the mutations identified. One case showed mutations in MEN1 and MLH1 and developed tumours associated with both cancer syndromes. Interestingly, three of the double mutants had a young age of onset or severe breast cancer phenotype and carried mutations in moderate to low-risk DNA damage repair-associated genes; two of them presented biallelic inactivation of CHEK2. We included these two patients for the sake of their clinical interest although we are aware that they do not exactly fulfil the definition of MINAS since both mutations are in the same gene. CONCLUSIONS AND RELEVANCE: Genetic analysis of a broad cancer gene panel identified the largest series of patients with MINAS described in a single study. Overall, our data do not support the existence of more severe manifestations in double mutants at the time of diagnosis although they do confirm previous evidence of severe phenotype in biallelic CHEK2 and other DNA repair cancer-predisposing genes.

Primary constitutional MLH1 epimutations: a focal epigenetic event.

BACKGROUND: Constitutional MLH1 epimutations are characterised by monoallelic methylation of the MLH1 promoter throughout normal tissues, accompanied by allele-specific silencing. The mechanism underlying primary MLH1 epimutations is currently unknown. The aim of this study was to perform an in-depth characterisation of constitutional MLH1 epimutations targeting the aberrantly methylated region around MLH1 and other genomic loci. METHODS: Twelve MLH1 epimutation carriers, 61 Lynch syndrome patients, and 41 healthy controls, were analysed by Infinium 450 K array. Targeted molecular techniques were used to characterise the MLH1 epimutation carriers and their inheritance pattern. RESULTS: No nucleotide or structural variants were identified in-cis on the epimutated allele in 10 carriers, in which inter-generational methylation erasure was demonstrated in two, suggesting primary type of epimutation. CNVs outside the MLH1 locus were found in two cases. EPM2AIP1-MLH1 CpG island was identified as the sole differentially methylated region in MLH1 epimutation carriers compared to controls. CONCLUSION: Primary constitutional MLH1 epimutations arise as a focal epigenetic event at the EPM2AIP1-MLH1 CpG island in the absence of cis-acting genetic variants. Further molecular characterisation is needed to elucidate the mechanistic basis of MLH1 epimutations and their heritability/reversibility.

Using Google Translate

INTRODUCTION: Doctor-patient communication is essential to the establishment of a therapeutic relationship and to the clinical improvement of the patient. Medical Interpreter Services (MIS) allow the doctors to communicate with patients that do not speak the same language of the clinical staff. However, MIS are not always available and when that happens it is of the upmost importance to find alternatives. OBJECTIVES AND METHODS: Presentation of a clinical case in which Google Translate^© (GT^©) was used as a translation tool to communicate with a patient. Discussion of the utility and validity of GT^© as a translation tool in Medicine. A Pubmed search for articles concerning the use of technological innovations as translation tools was performed using the key words: GT^©, language barriers, foreign language, and communication barriers. RESULTS: In the reported clinical case, GT^© allowed the translation and the establishment of communication with a foreign patient. The Pubmed search found two articles concerning the use and validity of GT^© as a translation tool in Medicine. CONCLUSIONS: GT^© is the most readily available and free initial mode of communication between a doctor and a patient when language is a barrier. Nonetheless, GT^

Investigating the effect of 28 BRCA1 and BRCA2 mutations on their related transcribed mRNA.

Germline inactivating mutations in the BRCA1 and BRCA2 genes are responsible for hereditary breast and ovarian cancer syndrome (HBOCS). Genetic testing of these genes identifies a significant proportion of variants of uncertain significance (VUS). Elucidation of the clinical impact of these variants is an important challenge in genetic diagnostics and counseling. In this study, we assess the RNA effect of 28 BRCA1 and BRCA2 VUS identified in our set of HBOCS families with the aim of gaining insight into their clinical relevance. mRNA was extracted from VUS carriers and controls lymphocytes cultured for 5-6 days and treated with puromycin. RNA was reverse transcribed to perform transcriptional analysis for the study of splicing aberrations. In silico prediction tools were used to select those variants most likely to affect the RNA splicing process. Six out of the 28 variants analyzed showed an aberrant splicing pattern and could therefore be classified as probably pathogenic mutations. Reclassification of VUS improves the genetic counseling and clinical surveillance of carriers of these mutations and highlights the importance of RNA studies in routine diagnostic laboratories.

Prevalence of germline MUTYH mutations among Lynch-like syndrome patients.

BACKGROUND AND AIMS: Individuals with tumours showing mismatch repair (MMR) deficiency not linked to germline mutations or somatic methylation of MMR genes have been recently referred as having 'Lynch-like syndrome' (LLS). The genetic basis of these LLS cases is unknown. MUTYH-associated polyposis patients show some phenotypic similarities to Lynch syndrome patients. The aim of this study was to investigate the prevalence of germline MUTYH mutations in a large series of LLS patients. METHODS: Two hundred and twenty-five probands fulfilling LLS criteria were included in this study. Screening of MUTYH recurrent mutations, whole coding sequencing and a large rearrangement analysis were undertaken. Age, sex, clinical, pathological and molecular characteristics of tumours including KRAS mutations were assessed. RESULTS: We found a prevalence of 3.1% of MAP syndrome in the whole series of LLS (7/225) and 3.9% when only cases fulfilling clinical criteria were considered (7/178). Patients with MUTYH biallelic mutations had more adenomas than monoallelic (P=0.02) and wildtype patients (P<0.0001). Six out of nine analysed tumours from six biallelic MUTYH carriers harboured KRAS-p.G12C mutation. This mutation was found to be associated with biallelic MUTYH germline mutation when compared with reported series of unselected colorectal cancer cohorts (P<0.0001). CONCLUSIONS: A proportion of unexplained LLS cases is caused by biallelic MUTYH mutations. The obtained results further justify the inclusion of MUTYH in the diagnostic strategy for Lynch syndrome-suspected patients.

ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes.

Next-generation sequencing (NGS) is changing genetic diagnosis due to its huge sequencing capacity and cost-effectiveness. The aim of this study was to develop an NGS-based workflow for routine diagnostics for hereditary breast and ovarian cancer syndrome (HBOCS), to improve genetic testing for BRCA1 and BRCA2. A NGS-based workflow was designed using BRCA MASTR kit amplicon libraries followed by GS Junior pyrosequencing. Data analysis combined Variant Identification Pipeline freely available software and ad hoc R scripts, including a cascade of filters to generate coverage and variant calling reports. A BRCA homopolymer assay was performed in parallel. A research scheme was designed in two parts. A Training Set of 28 DNA samples containing 23 unique pathogenic mutations and 213 other variants (33 unique) was used. The workflow was validated in a set of 14 samples from HBOCS families in parallel with the current diagnostic workflow (Validation Set). The NGS-based workflow developed permitted the identification of all pathogenic mutations and genetic variants, including those located in or close to homopolymers. The use of NGS for detecting copy-number alterations was also investigated. The workflow meets the sensitivity and specificity requirements for the genetic diagnosis of HBOCS and improves on the cost-effectiveness of current approaches.

MLH1 methylation screening is effective in identifying epimutation carriers.

Recently, constitutional MLH1 epimutations have been identified in a subset of Lynch syndrome (LS) cases. The aim of this study was the identification of patients harboring constitutional MLH1 epimutations in a set of 34 patients with a clinical suspicion of LS, MLH1-methylated tumors and non-detected germline mutations in mismatch repair (MMR) genes. MLH1 promoter methylation was analyzed in lymphocyte DNA samples by MS-MLPA (Methylation-specific multiplex ligation-dependent probe amplification). Confirmation of MLH1 constitutional methylation was performed by MS-MCA (Methylation-specific melting curve analysis), bisulfite sequencing and pyrosequencing in different biological samples. Allelic expression was determined using heterozygous polymorphisms. Vertical transmission was evaluated by MS-MLPA and haplotype analyses. MS-MLPA analysis detected constitutional MLH1 methylation in 2 of the 34 individuals whose colorectal cancers showed MLH1 methylation (5.9%). These results were confirmed by bisulfite-based methods. Both epimutation carriers had developed metachronous early-onset LS tumors, with no family history of LS-associated cancers in their first-degree relatives. In one of the cases, the identified MLH1 constitutional methylation was monoallelic and results in MLH1 and EPM2AIP1 allele-specific transcriptional silencing. It was present in normal somatic tissues and absent in spermatozoa. The methylated MLH1 allele was maternally transmitted and methylation was reversed in a daughter who inherited the same allele. MLH1 methylation screening in lymphocyte DNA from patients with early-onset MLH1-methylated LS-associated tumors allows the identification of epimutation carriers. The present study adds further evidence to the emerging entity of soma-wide MLH1 epimutation and its heritability.

Identification of a new complex rearrangement affecting exon 20 of BRCA1.

In this study, we present a novel complex rearrangement in the BRCA1 gene. The genomic rearrangement was identified using one of the two commercially available MLPA BRCA1 kits but was not confirmed with the other. In this report, we present the full characterization at the DNA and RNA levels of a new partial deletion of exon 20 of BRCA1. This is a complex deletion with four breakpoints which promotes aberrant splicing with partial deletion of exon 20 plus the insertion of a cryptic exon corresponding to a fragment of intron 20. The aberrant splicing generates an abnormal transcript with a frameshift that will result in a truncated BRCA1 protein.

Detection of APC gene deletions using quantitative multiplex PCR of short fluorescent fragments.

BACKGROUND: approximately 20% of classic familial adenomatous polyposis (FAP) cases and 70% to 80% of attenuated FAP (AFAP) cases are negative for the APC/MUTYH point mutation. Quantitative multiplex PCR of short fluorescent fragments (QMPSF), a technique for detecting copy number alterations, has been successfully applied to several cancer syndrome genes. We used QMPSF for the APC gene to screen FAP APC/MUTYH mutation-negative families to improve their diagnostic surveillance. METHODS: we set up and validated APC-gene QMPSF using 23 negative and 1 positive control and examined 45 (13 FAP and 32 AFAP) unrelated members of APC/MUTYH mutation-negative families for copy number alterations. We confirmed the results using multiplex ligation-dependent probe amplification (MLPA). We used different approaches such as sequencing, quantitative real time-PCR (QRT-PCR), and fluorescence in situ hybridization (FISH) to further characterize the identified deletions. RESULTS: APC QMPSF was capable of detecting deletions with an acceptable variability, as shown by mean values (SD) of allele dosage for the deleted control obtained from intra- and interexperimental replicates [0.52 (0.05) and 0.45 (0.10)]. We detected 3 gross deletions in 13 (23%) of the classic FAP cases analyzed (1 complete gene deletion and 2 partial deletions encompassing exons 9 and 10 and exons 11-15, respectively). No rearrangements were detected in the 32 AFAP cases. CONCLUSIONS: QMPSF is able to detect rearrangements of the APC gene. Our findings highlight the importance of using a copy number alteration methodology as a first step in the routine genetic testing of FAP families in the clinical setting.