A Pathogenic Mosaic TP53 Mutation in Two Germ Layers Detected by Next Generation Sequencing

Background

Li-Fraumeni syndrome is caused by germline TP53 mutations and is clinically characterized by a predisposition to a range of cancers, most commonly sarcoma, brain tumours and leukemia. Pathogenic mosaic TP53 mutations have only rarely been described.

Methods and Findings

We describe a 2 years old child presenting with three separate cancers over a 6 month period; two soft tissue mesenchymal tumors and an aggressive metastatic neuroblastoma. As conventional testing of blood DNA by Sanger sequencing for mutations in TP53, ALK, and SDH was negative, whole exome sequencing of the blood DNA of the patient and both parents was performed to screen more widely for cancer predisposing mutations. In the patient''s but not the parents'' DNA we found a c.743 G>A, p.Arg248Gln (CCDS11118.1) TP53 mutation in 3–20% of sequencing reads, a level that would not generally be detectable by Sanger sequencing. Homozygosity for this mutation was detected in all tumor samples analyzed, and germline mosaicism was demonstrated by analysis of the child''s newborn blood spot DNA. The occurrence of separate tumors derived from different germ layers suggests that this de novo mutation occurred early in embryogenesis, prior to gastrulation.

Conclusion

The case demonstrates pathogenic mosaicim, detected by next generation deep sequencing, that arose in the early stages of embryogenesis.     

Next Generation Sequencing in der diagnostischen Praxis

Next generation sequencing (NGS) allows whole exome or whole genome sequencing for a given patient to be performed timely and at reasonable cost. This diagnostic quantum leap not only has various legal, ethical and economical aspects but will naturally also impact upon patient care. Currently, however, the wide-spread introduction of NGS into routine diagnostics is facing many obstacles. In particular, it is to be expected that NGS will identify a large number of rare variants in a given patient that are of (yet) unknown clinical significance. As a first step towards solving this problem, we introduce the concept of a database that will systematically integrate genotypic and phenotypic information from the German health care context. Not only will this resource be of great scientific value, but the database shall also provide human geneticists with the evidence base necessary for the reliable evaluation of their patient-related sequencing data.     

Short Barcodes for Next Generation Sequencing

We consider the design and evaluation of short barcodes, with a length between six and eight nucleotides, used for parallel sequencing on platforms where substitution errors dominate. Such codes should have not only good error correction properties but also the code words should fulfil certain biological constraints (experimental parameters). We compare published barcodes with codes obtained by two new constructions methods, one based on the currently best known linear codes and a simple randomized construction method. The evaluation done is with respect to the error correction capabilities, barcode size and their experimental parameters and fundamental bounds on the code size and their distance properties. We provide a list of codes for lengths between six and eight nucleotides, where for length eight, two substitution errors can be corrected. In fact, no code with larger minimum distance can exist.     

Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data

Noncoding DNA sequences (NCS) have attracted much attention recently due to their functional potentials. Here we attempted to reveal the functional roles of noncoding sequences from the point of view of natural selection that typically indicates the functional potentials of certain genomic elements. We analyzed nearly 37 million single nucleotide polymorphisms (SNPs) of Phase I data of the 1000 Genomes Project. We estimated a series of key parameters of population genetics and molecular evolution to characterize sequence variations of the noncoding genome within and between populations, and identified the natural selection footprints in NCS in worldwide human populations. Our results showed that purifying selection is prevalent and there is substantial constraint of variations in NCS, while positive selectionis more likely to be specific to some particular genomic regions and regional populations. Intriguingly, we observed larger fraction of non-conserved NCS variants with lower derived allele frequency in the genome, indicating possible functional gain of non-conserved NCS. Notably, NCS elements are enriched for potentially functional markers such as eQTLs, TF motif, and DNase I footprints in the genome. More interestingly, some NCS variants associated with diseases such as Alzheimer''s disease, Type 1 diabetes, and immune-related bowel disorder (IBD) showed signatures of positive selection, although the majority of NCS variants, reported as risk alleles by genome-wide association studies, showed signatures of negative selection. Our analyses provided compelling evidence of natural selection forces on noncoding sequences in the human genome and advanced our understanding of their functional potentials that play important roles in disease etiology and human evolution.     

Impact of Next Generation Sequencing Techniques in Food Microbiology

Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.     

Molecular Diagnosis of Putative Stargardt Disease by Capture Next Generation Sequencing

Stargardt Disease (STGD) is the commonest genetic form of juvenile or early adult onset macular degeneration, which is a genetically heterogeneous disease. Molecular diagnosis of STGD remains a challenge in a significant proportion of cases. To address this, seven patients from five putative STGD families were recruited. We performed capture next generation sequencing (CNGS) of the probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes. Seven disease-causing mutations in ABCA4 and two in PROM1 were identified by CNGS, which provides a confident genetic diagnosis in these five families. We also provided a genetic basis to explain the differences among putative STGD due to various mutations in different genes. Meanwhile, we show for the first time that compound heterozygous mutations in PROM1 gene could cause cone-rod dystrophy. Our findings support the enormous potential of CNGS in putative STGD molecular diagnosis.     

ANGSD: Analysis of Next Generation Sequencing Data

Background

High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously.

Results

We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods.

Conclusions

The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd. The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0356-4) contains supplementary material, which is available to authorized users.     

高通量测序技术在农作物全基因组序列测定中的应用概览

近几年飞速发展的高通量测序技术(next generation sequencing,NGS)在生命科学研究的各个领域充分展现了其低成本、高通量和应用面广等优势。在现代农业生物技术领域,利用高通量测序技术,科学家们不仅能更经济而高效对农作物、模式植物或不同栽培品种进行深入的全基因组测序、重测序,也可以对成百上千的栽培品种进行高效而准确的遗传差异分析、分子标记分析、连锁图谱分析、表观遗传学分析、转录组分析,进而改进农作物的育种技术,加快新品种的育种研究。其中,获得农作物的全基因组序列是其他研究和分析的基础。本文通过介绍近年来发表的一些利用高通量测序技术进行的农作物全基因组测定和组装的工作,展示高通量测序技术在现代农业生物技术领域的广泛前景以及其建立起来的研究基础。     

二代及三代测序技术在遗传学诊断中的应用进展

遗传病的防治是公共卫生领域的重大课题,而明确病因是遗传病防治的重要环节。高通量测序技术（又称二代测序技术）具有高通量、低成本、高准确度的优点,为遗传诊断及咨询提供了直接证据,已成为遗传学检测不可或缺的有力工具;第三代测序也凭借其长读长的独特优势在临床应用中占据一席之地。二代及三代测序技术各有特点,互为补充,临床中针对不同的检测需求有多种类型的测序方案可供选择。基于此,对二代及三代测序技术的原理、分类及其在遗传学诊断中的应用进展做一综述,以期为临床测序方案的选择提供思路和指导。     

第二代测序在检测人类基因突变中的应用

很多的人类疾病与基因突变有关,基因突变在疾病的诊断和治疗中起到了至关重要的作用.第二代高通量测序,其特点为通量高、速度快、成本低,给检测基因突变带来了革命性的变化.该技术检测基因突变的流程简单,研究人员运用全基因组从测序,目标基因组测序以及转录组测序能够实现基因突变的全方位、高准确的检测.     

Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat

With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat ( Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat.