Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization.

BACKGROUND: Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base-pair resolution, but the use of short-read sequencing is limited by repetitive sequences, and long-read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked-reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short-read to linked-read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short-read WGS. METHODS: We included 13 patients carrying various SVs. Whole genome analyses were performed using paired-end HiSeq X sequencing with (linked-read strategy) or without (short-read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short-read strategy and LongRanger for long-read strategy. Variant interpretations were first blinded. RESULTS: The short-read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked-read strategy identified 10/13 SVs, including one (patient 7) missed by the short-read strategy. CONCLUSION: In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV.

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers.

INTRODUCTION: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. METHODS: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. RESULTS: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. CONCLUSIONS: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.

Binary mesh partitioning for cache-efficient visualization.

One important bottleneck when visualizing large data sets is the data transfer between processor and memory. Cache-aware (CA) and cache-oblivious (CO) algorithms take into consideration the memory hierarchy to design cache efficient algorithms. CO approaches have the advantage to adapt to unknown and varying memory hierarchies. Recent CA and CO algorithms developed for 3D mesh layouts significantly improve performance of previous approaches, but they lack of theoretical performance guarantees. We present in this paper a {\schmi O}(N\log N) algorithm to compute a CO layout for unstructured but well shaped meshes. We prove that a coherent traversal of a N-size mesh in dimension d induces less than N/B+{\schmi O}(N/M;{1/d}) cache-misses where B and M are the block size and the cache size, respectively. Experiments show that our layout computation is faster and significantly less memory consuming than the best known CO algorithm. Performance is comparable to this algorithm for classical visualization algorithm access patterns, or better when the BSP tree produced while computing the layout is used as an acceleration data structure adjusted to the layout. We also show that cache oblivious approaches lead to significant performance increases on recent GPU architectures.

On the use of phylogeny-based tests to detect association between quantitative traits and haplotypes.

With the increasing availability of genetic data, several SNPs in a candidate gene can be combined into haplotypes to test for association with a quantitative trait. When the number of SNPs increases, the number of haplotypes can become very large and there is a need to group them together. The use of the phylogenetic relationships between haplotypes provides a natural and efficient way of grouping. Moreover, it allows us to identify disease or quantitative trait-related loci. In this article, we describe ALTree-q, a phylogeny-based approach to test for association between quantitative traits and haplotypes and to identify putative quantitative trait nucleotides (QTN). This study focuses on ALTree-q association test which is based on one-way analyses of variance (ANOVA) performed at the different levels of the tree. The statistical properties (type-one error and power rates) were estimated through simulations under different genetic models and were compared to another phylogeny-based test, TreeScan, (Templeton, 2005) and to a haplotypic omnibus test consisting in a one-way ANOVA between all haplotypes. For dominant and additive models ALTree-q is usually the most powerful test whereas TreeScan performs better under a recessive model. However, power depends strongly on the recurrence rate of the QTN, on the QTN allele frequency, and on the linkage disequilibrium between the QTN and other markers. An application of the method on Thrombin Activatable Fibronolysis Inhibitor Antigen levels in European and African samples confirms a possible association with polymorphisms of the CPB2 gene and identifies several QTNs.

ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees.

Finding the genes involved in complex diseases susceptibility and among those genes, localizing the variant sites explaining this susceptibility is a major goal of genetic epidemiology. In this context, haplotypic methods that use the joint information on several markers may be of particular interest. When the number of haplotypes is large, a grouping may be required. Phylogenetic trees allow such groupings of haplotypes based on their evolutionary history and may help in the detection and localization of disease susceptibility sites. In this paper, we present a new software to perform phylogeny-based association and localization analysis.

On the use of haplotype phylogeny to detect disease susceptibility loci.

BACKGROUND: The cladistic approach proposed by Templeton has been presented as promising for the study of the genetic factors involved in common diseases. This approach allows the joint study of multiple markers within a gene by considering haplotypes and grouping them in nested clades. The idea is to search for clades with an excess of cases as compared to the whole sample and to identify the mutations defining these clades as potential candidate disease susceptibility sites. However, the performance of this approach for the study of the genetic factors involved in complex diseases has never been studied. RESULTS: In this paper, we propose a new method to perform such a cladistic analysis and we estimate its power through simulations. We show that under models where the susceptibility to the disease is caused by a single genetic variant, the cladistic test is neither really more powerful to detect an association nor really more efficient to localize the susceptibility site than an individual SNP testing. However, when two interacting sites are responsible for the disease, the cladistic analysis greatly improves the probability to find the two susceptibility sites. The impact of the linkage disequilibrium and of the tree characteristics on the efficiency of the cladistic analysis are also discussed. An application on a real data set concerning the CARD15 gene and Crohn disease shows that the method can successfully identify the three variant sites that are involved in the disease susceptibility. CONCLUSION: The use of phylogenies to group haplotypes is especially interesting to pinpoint the sites that are likely to be involved in disease susceptibility among the different markers identified within a gene.