a. We recommend that the standard methodology for genetic diagnosis of autosomal dominant polycystic kidney disease is polymerase chain reaction (PCR) amplification (including long-range PCR for the first 33 exons of PKD1) followed by Sanger sequencing (1A) or next-generation sequencing where available (1D). b. We suggest that individuals with a clinical diagnosis of autosomal dominant polycyst...

Significant advances in our knowledge of cancer genomes are rapidly changing the way we think about tumor biology and the heterogeneity of cancer. Recent successes in genomically-guided treatment approaches accompanied by more sophisticated sequencing techniques have paved the way for deeper investigation into the landscape of genomic rearrangements in cancer. While considerable research on sol...

UNLABELLED Pancreatic acinar cell carcinomas (PACC) account for approximately 1% (∼500 cases) of pancreatic cancer diagnoses annually in the United States. Oncogenic therapuetic targets have proven elusive in this disease, and chemotherapy and radiotherapy have demonstrated limited efficacy against these tumors. Comprehensive genomic profiling of a large series of PACCs (n=44) identified recurr...

AIM To identify cryptic subtelomeric rearrangement, a possible cause of idiopathic mental retardation by means of multiprobe telomere fluorescent in situ hybridization (T-FISH). METHODS Hundred patients (median age 3.0 years) with mental retardation and dysmorphic features were screened using specific T-FISH probes. Multiplex ligation-dependent probe amplification and comparative genomic hybr...

3. Nadeau JH, Taylor BA “Lengths of chromosomal segments conserved since divergence of man and mouse” Proc. Natl. Acad. Sci, 81(814-818), 1984 4. Wienberg J ‘The evolution of eutherian chromosomes” Curr. Opin. Genet. Dev. 14(657666), 2004 5. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Argawala R, Ainscough R, Alexandersson M, An P “Initial sequencing and comparative a...

UNLABELLED We present a graphical tool dedicated to the exploration of bacterial genome rearrangements. The principle of this exploration relies on the reconstruction of ancestral genomes at each internal node of a gene-order-based phylogenetic tree. This tool allows the selection of internal nodes to visualize the rearrangements between the inferred chromosome of this node and its direct desce...

The phosphatase and tensin homolog gene (PTEN) on chromosome 10q23.3 is a negative regulator of the PIK3/Akt survival pathway and is the most frequently deleted tumor suppressor gene in prostate cancer. Monoallelic loss of PTEN is present in up to 60% of localized prostate cancers and complete loss of PTEN in prostate cancer is linked to metastasis and androgen-independent progression. Studies ...

We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature de...

MOTIVATION The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequen...

Background. Why only some bacteria isolated from mixed populations predominate or become infectious is incompletely understood, although ecological interactions of communities of bacteria referred to as the microbiome is gaining popularity as one explanation. We hypothesized that whole genome mapping (WGM) and sequencing (WGS) could reveal metagenomic differences pertinent to this phenomenon. M...