Next-generation Genome Analysis Research Articles

Wild-type APC and prognosis in metastatic colorectal cancer.

223 Background: Somatic mutations at adenomatous polyposis coli ( APC) gene, found in ~75% of colorectal cancers (CRC), are under-represented in microsatellite instable (MSI-H) tumors. While several studies have suggested worse outcomes for CRC patients (pts) with wild-type APC ( APC-WT), the prognostic implication of this genomic alteration in metastatic CRC (mCRC) is not well defined. Methods: APC prognostic value was evaluated in 331 stage IV microsatellite stable (MSS) CRC pts treated in our institution. Next-generation genomic analysis (FoundationOne) was used to characterize the molecular characteristics of APC-WT and mutant APC ( APC-MT) pts. Findings were validated on a public database of stage IV colon cancer from MSKCC. Results: APC-WT was present in 26% of mCRC patients. In comparison to APC-MT population (n = 244), APC-WT pts (n = 87) tended to be younger (median age: 49 vs. 58 years), right-sided (44% vs. 24%), BRAF-V600E mutated (25% vs. 5%), p53 WT (38% vs. 21%) and RAS WT (66% vs. 53%). APC-WT tumors were associated with other Wnt activating alterations ( CTNNB1, FBXW7, RNF43, ARID1A and SOX9). Among those, RNF43 and CTNNB1 were more significantly represented in the APC-WT vs APC-MT population (12% vs 1% and 11% vs 3%, respectively). APC-WT pts had a worse overall survival (OS) than APC-MT pts (30 vs 48 months, HR = 1.809, 95% CI 1.260-2.596, p < 0.0001). Using a multivariate model correcting for primary tumor location, RAS and BRAF status, APC-WT was predictive of poor survival (HR = 1.7, p = 0.001) in our data set. The prognostic implication of APC-WT on OS were confirmed further in a similar multivariate model of 433 stage IV pts from MSKCC public database (HR = 1.6, P = 0.01). Conclusions: APC-WT is associated with poor OS in MSS mCRC regardless of RAS, BRAF status. Compared with APC-MT mCRC tumors, APC-WT tumors were associated with other activating alterations of Wnt pathway, including RNF43 and CTNBB1.

A novel method for functional annotation prediction based on combination of classification methods.

Automated protein function prediction defines the designation of functions of unknown protein functions by using computational methods. This technique is useful to automatically assign gene functional annotations for undefined sequences in next generation genome analysis (NGS). NGS is a popular research method since high-throughput technologies such as DNA sequencing and microarrays have created large sets of genes. These huge sequences have greatly increased the need for analysis. Previous research has been based on the similarities of sequences as this is strongly related to the functional homology. However, this study aimed to designate protein functions by automatically predicting the function of the genome by utilizing InterPro (IPR), which can represent the properties of the protein family and groups of the protein function. Moreover, we used gene ontology (GO), which is the controlled vocabulary used to comprehensively describe the protein function. To define the relationship between IPR and GO terms, three pattern recognition techniques have been employed under different conditions, such as feature selection and weighted value, instead of a binary one.

PolyCat: A Resource for Genome Categorization of Sequencing Reads From Allopolyploid Organisms

Read mapping is a fundamental part of next-generation genomic research but is complicated by genome duplication in many plants. Categorizing DNA sequence reads into their respective genomes enables current methods to analyze polyploid genomes as if they were diploid. We present PolyCat—a pipeline for mapping and categorizing all types of next-generation sequence data produced from allopolyploid organisms. PolyCat uses GSNAP’s single-nucleotide polymorphism (SNP)-tolerant mapping to minimize the mapping efficiency bias caused by SNPs between genomes. PolyCat then uses SNPs between genomes to categorize reads according to their respective genomes. Bisulfite-treated reads have a significant reduction in nucleotide complexity because nucleotide conversion events are confounded with transition substitutions. PolyCat includes special provisions to properly handle bisulfite-treated data. We demonstrate the functionality of PolyCat on allotetraploid cotton, Gossypium hirsutum, and create a functional SNP index for efficiently mapping sequence reads to the D-genome sequence of G. raimondii. PolyCat is appropriate for all allopolyploids and all types of next-generation genome analysis, including differential expression (RNA sequencing), differential methylation (bisulfite sequencing), differential DNA-protein binding (chromatin immunoprecipitation sequencing), and population diversity.

From genes to function: theC.elegansgenetic toolbox

This review aims to provide an overview of the technologies which make the nematode Caenorhabditis elegans an attractive genetic model system. We describe transgenesis techniques and forward and reverse genetic approaches to isolate mutants and clone genes. In addition, we discuss the new possibilities offered by genome engineering strategies and next-generation genome analysis tools.

The genetics of attention deficit/hyperactivity disorder in adults, a review

The adult form of attention deficit/hyperactivity disorder (aADHD) has a prevalence of up to 5% and is the most severe long-term outcome of this common neurodevelopmental disorder. Family studies in clinical samples suggest an increased familial liability for aADHD compared with childhood ADHD (cADHD), whereas twin studies based on self-rated symptoms in adult population samples show moderate heritability estimates of 30–40%. However, using multiple sources of information, the heritability of clinically diagnosed aADHD and cADHD is very similar. Results of candidate gene as well as genome-wide molecular genetic studies in aADHD samples implicate some of the same genes involved in ADHD in children, although in some cases different alleles and different genes may be responsible for adult versus childhood ADHD. Linkage studies have been successful in identifying loci for aADHD and led to the identification of LPHN3 and CDH13 as novel genes associated with ADHD across the lifespan. In addition, studies of rare genetic variants have identified probable causative mutations for aADHD. Use of endophenotypes based on neuropsychology and neuroimaging, as well as next-generation genome analysis and improved statistical and bioinformatic analysis methods hold the promise of identifying additional genetic variants involved in disease etiology. Large, international collaborations have paved the way for well-powered studies. Progress in identifying aADHD risk genes may provide us with tools for the prediction of disease progression in the clinic and better treatment, and ultimately may help to prevent persistence of ADHD into adulthood.

InGAP: an integrated next-generation genome analysis pipeline

Summary: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length. Experiments on simulated and experimental data show that this pipeline can achieve overall 97% accuracy in SNP detection and 94% in the finding of indels. All the detected SNPs/indels can be further evaluated by a graphical editor in our pipeline. inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly.Availability: inGAP is available at http://sites.google.com/site/nextgengenomics/ingapContact: scs@bx.psu.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Novel Convective Flow Based Approaches for High-Throughput PCR Thermocycling

A critical need exists for the development of next-generation genomic analysis instrumentation capable of offering significantly higher throughput at a lower cost than current technology. In this paper, we explore the potential of natural convection-based systems to address these issues by providing a thermocycling hardware platform capable of performing rapid polymerase chain reaction (PCR) amplification of DNA. These systems can be arrayed in a multi-well format that is simple to operate, is suitable for integration with high-throughput automated liquid handling systems, and can be easily and inexpensively mass-produced.