Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage

Advantages and diagnostic effectiveness of the two most widely used resequencing approaches, whole exome (WES) and whole genome (WGS) sequencing, are often debated. WES dominated large-scale resequencing projects because of lower cost and easier data storage and processing. Rapid development of 3(rd) generation sequencing methods and novel exome sequencing kits predicate the need for a robust statistical framework allowing informative and easy performance comparison of the emerging methods. In our study we developed a set of statistical tools to systematically assess coverage of coding regions provided by several modern WES platforms, as well as PCR-free WGS. We identified a substantial problem in most previously published comparisons which did not account for mappability limitations of short reads. Using regression analysis and simple machine learning, as well as several novel metrics of coverage evenness, we analyzed the contribution from the major determinants of CDS coverage. Contrary to a common view, most of the observed bias in modern WES stems from mappability limitations of short reads and exome probe design rather than sequence composition. We also identified the similar to 500kb region of human exome that could not be effectively characterized using short read technology and should receive special attention during variant analysis. Using our novel metrics of sequencing coverage, we identified main determinants of WES and WGS performance. Overall, our study points out avenues for improvement of enrichment-based methods and development of novel approaches that would maximize variant discovery at optimal cost

Мультиспиральная компьютерная томография с контрастным усилением в оценке степени злокачественности светлоклеточного рака почки

Objective: to determine the effectiveness of multidetector commuted tomography (MDCT) for evaluating the grading (Fuhrman grade) of clear cell renal cell carcinoma (CCRCC) Materials and methods. Four-phase contrast-enhanced MDCT of 54 patients with histologically verified clear cell renal carcinoma operated on in A.V. Vishnevsky Institute of Surgery from April 2011 to March 2015 have been retrospectively analyzed. The patients were divided in two groups based on Furhman grade (1982). The first Group included Grade I and Grade II (n = 37). The second group included Grade III and Grade IV tumors (n = 17). Contrast enhancement was calculated for each group via manual ROI placement in arterial, portal, delayed phases and averaging tumor density. The non-parametric Mann-Whitney U test and Fisher criterion were used to determine whether there was a significant correlation between contrast enhancement and Fuhrman grade; p value of 80 HU) (p 80 ед.Н) с вымыванием его к выделительной фазе; инвазия образований в капсулу почки и выход за ее пределы встречаются реже. Низкодифференцированные светлоклеточные раки почки имеют: достоверно больший размер (р 60 мм); нечеткие неровные контуры образования; структура опухолей гетерогенна за счет наличия некрозов и кровоизлияний в строме опухоли; достоверно меньше (р < 0,05) накапливают контрастный препарат в артериальную и венозную фазы (показатели ед.Н в артериальную и венозную фазы ниже в связи с тем, что большое количество некрозов и кровоизлияний в структуре опухоли), вымывание в выделительную фазу происходит медленно и неравномерно; инвазия образований в капсулу почки и выход за ее пределы встречаются достоверно чаще (р < 0,05); также достоверно чаще встречаются опухолевые тромбы в почечной и нижней полой венах (р < 0,05). Выводы. Определены параметры, позволяющие при КТ-исследовании с большей долей вероятности дифференцировать степень злокачественности светлоклеточного рака почки

Analytical “Bake-Off” of Whole Genome Sequencing Quality for the Genome Russia Project Using a Small Cohort for Autoimmune Hepatitis

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case’s unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (FTCD), plus multiple occurrences of known HLA-DRB1 alleles associated with AIH (HLA-DRB1-03:01:01, 13:01:01 and 7:01:01). We also list putative SNVs in other genes as suggestive in AIH influence

Identification of Novel Candidate Markers of Type 2 Diabetes and Obesity in Russia by Exome Sequencing with a Limited Sample Size

Type 2 diabetes (T2D) and obesity are common chronic disorders with multifactorial etiology. In our study, we performed an exome sequencing analysis of 110 patients of Russian ethnicity together with a multi-perspective approach based on biologically meaningful filtering criteria to detect novel candidate variants and loci for T2D and obesity. We have identified several known single nucleotide polymorphisms (SNPs) as markers for obesity (rs11960429), T2D (rs9379084, rs1126930), and body mass index (BMI) (rs11553746, rs1956549 and rs7195386) (p &lt; 0.05). We show that a method based on scoring of case-specific variants together with selection of protein-altering variants can allow for the interrogation of novel and known candidate markers of T2D and obesity in small samples. Using this method, we identified rs328 in LPL (p = 0.023), rs11863726 in HBQ1 (p = 8 &times; 10&minus;5), rs112984085 in VAV3 (p = 4.8 &times; 10&minus;4) for T2D and obesity, rs6271 in DBH (p = 0.043), rs62618693 in QSER1 (p = 0.021), rs61758785 in RAD51B (p = 1.7 &times; 10&minus;4), rs34042554 in PCDHA1 (p = 1 &times; 10&minus;4), and rs144183813 in PLEKHA5 (p = 1.7 &times; 10&minus;4) for obesity; and rs9379084 in RREB1 (p = 0.042), rs2233984 in C6orf15 (p = 0.030), rs61737764 in ITGB6 (p = 0.035), rs17801742 in COL2A1 (p = 8.5 &times; 10&minus;5), and rs685523 in ADAMTS13 (p = 1 &times; 10&minus;6) for T2D as important susceptibility loci in Russian population. Our results demonstrate the effectiveness of whole exome sequencing (WES) technologies for searching for novel markers of multifactorial diseases in cohorts of limited size in poorly studied populations

Genome-wide sequence analyses of ethnic populations across Russia

The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show allele frequency divergence from neighboring populations. Population genetics analyses revealed six phylogeographic partitions among indigenous ethnicities corresponding to their geographic locales. This study presents a characterization of population-specific genomic variation in Russia with results important for medical genetics and for understanding the dynamic population history of the world's largest country