Evaluation of the Ion Torrent PGM sequencing workflow for the routine rapid detection of BRCA1 and BRCA2 germline mutations.

PURPOSE: Conventional methods used to identify BRCA1/2 germline mutations in hereditary cancers are time-consuming and expensive, due to the large size of the genes. The recent introduction of next generation sequencing (NGS) benchtop platforms is a great promise, which is rapidly revolutionizing genetic screening in diagnostic and clinical applications. We recently transferred our methodology for routine BRCA1/2 mutation screening (denaturing High Performance Liquid Chromatography plus Sanger sequencing) to the Ion Torrent PGM platform with the Ion Ampliseq BRCA1 and BRCA2 panel and tested the performance of the system. METHODS: We first validated the NGS approach in a cohort of 33 patients who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we tested 29 newly diagnosed and uncharacterized patients by NGS, and Sanger sequencing was used to confirm results from the NGS platform. RESULTS: In the validation cohort, all previously identified single nucleotide variants, insertions and deletions (also composed of multiple bases and within complex homopolymeric stretches) were identified by NGS in their correct zygosity status except for variants in a complex multinucleotide region within intron 7 of BRCA1 gene. NGS approach was further able to identify previously undetected variants. In the prospective cohort, almost all (99.3%) called variants were confirmed by Sanger. In both cohorts, in addition to the false positive (31) and false negative (110) results in the intron 7 of BRCA1 gene, the NGS method detected 10 false positives, that were solved by Sanger. CONCLUSIONS: The Ion Torrent PGM NGS approach in BRCA1/2 germline mutation identification is highly sensitive, easy to use, faster and cheaper than traditional approaches. Therefore, according to other recently published works, we highly recommend this system for routine diagnostic testing on BRCA1/2 genes, along with Sanger confirmation of the called variants, and support the usefulness of the approach also in other routine genetic analysis.

Familial exudative vitreoretinopathy caused by a homozygous mutation in TSPAN12 in a cystic fibrosis infant.

Familial exudative vitreoretinopathy (FEVR) is a genetic disease affecting the vascularization of the peripheral retina. The clinical manifestations are very heterogeneous, ranging from mildly affected patients, who could present no visual defects, to severe conditions which can also cause complete blindness at birth or in the first decade. FEVR can be inherited in all the three genetic forms: dominant, recessive and X-linked. To date, four genes have been associated with the condition: TSPAN12. NDP. FDZ4 and LRP5. Interestingly, mutations in TSPAN12 have been considered causative of both a dominant and recessive inheritance and a FEVR phenotype sensitive to the number of TSPAN12 mutations has been supposed. Here we describe a case of a female infant affected by cystic fibrosis and by a severe form of exudative vitreoretinopathy. In particular, we have detected the homozygous missense mutation c.668 T > C in TSPAN12. Neither of the heterozygous parents has ocular manifestations of the disease, suggesting a classic recessive mendelian pattern of inheritance.

18q deletion in a cystic fibrosis infant, increased morbidity and challenge for correct treatment choices: a case report.

Cystic Fibrosis (CF) is the most frequent recessive disease of Caucasian patients. Association with other diseases or syndromes has previously been reported. Co-morbidity may be a challenge for clinicians, who have to face more severe problems. We have described a CF infant, F508del homozygote, diagnosed by neonatal screening, who also had a chromosome 18q terminal deletion [del (18)(q22-qter)]. Some clinical features of the 18q deletion: e.g., cardiopathy, gastro-oesophageal reflux and severe muscular hypotonia, worsened the CF clinical picture and his quality of life, with repeated pulmonary exacerbations and failure to thrive in the first six months of life. The treatment strategy was chosen following an accurate multi-disciplinary team study of overlapping chromosome syndrome and CF symptoms. The use of a gastrostomy device for enteral nutrition together with a new device (Ez-PAP) for chest physiotherapy led to normal growth, a notably reduced hospitalization rate and improved quality of life. This case shows how co-morbidities worsening the clinical course of a "complicated patient" can be faced thanks to unconventional therapies that represent a challenge for clinicians.

CFTR mutation in an Arab patient: clinical and functional features of 875+1G-->A/875+1G-->A genotype.

Cystic fibrosis (CF; MIM# 219700) is the most frequent recessive disease in Caucasian patients. However, immigration from the Middle East and Africa to Europe is revealing different CFTR mutations. Here, we have described an 875+1G-->A mutation, found for the first time in a homozygous state in an 8 yr old boy. He was the child of a couple of Egyptian first level cousins, both carriers of the mutation. The functional test revealed the 875+1G-->A to be a severe mutation, leading to defective protein function as detected by nasal potential difference (NPD) measurements.

Identification of a new mutation in the SRY gene in a 46,XY woman with Swyer syndrome.

OBJECTIVE: To determine the genetic cause of primary amenorrhea in a 46,XY woman. DESIGN: Case report. SETTING: Centre of Gynecological Endocrinology and Cytogenetics and Molecular Genetics Laboratory of university medical school. PATIENT(S): A 19-year-old woman referred for primary amenorrhea. INTERVENTION(S): Clinical, endocrinologic, and ultrasonographic investigation and SRY mutation analysis. MAIN OUTCOME MEASURE(S): Hormone profile (LH, FSH, PRL, leptin, E(2), 17alpha-hydroxyprogesterone, 3alpha-androstanediol glucuronide), ultrasonographic evaluation, clinical follow-up. RESULT(S): A new SRY sporadic mutation due to a single nucleotide insertion at codon 13 position 38 (38-39insA) was found in a 46,XY woman with sex reversal. This mutation determined a frameshift of the reading frame sequence and a protein truncation at codon 16. Clinical and endocrinologic data are reported. CONCLUSION(S): This is a new rare case of a single nucleotide insertion affecting the SRY gene in 46,XY females with sex reversal. This new mutation should be considered in genetic counseling.