Next-generation sequencing-based genome diagnostics across clinical genetics centers: Implementation choices and their effects

Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patients with cardiomyopathy. We highlight critical implementation choices, including the specific contributions of laboratory and medical specialists, bioinformaticians and researchers to diagnostic genome care, and how these affect interpretation and reporting of variants. Reported pathogenic mutations were consistent for all but one patient. Of the two centers that were inconsistent in their diagnosis, one reported to have found 'no causal variant', thereby underdiagnosing this patient. The other provided an alternative diagnosis, identifying another variant as causal than the other centers. Ethical and legal analysis showed that informed consent procedures in all centers were generally adequate for diagnostic NGS applications that target a limited set of genes, but not for exome- and genome-based diagnosis. We propose changes to further improve and align these procedures, taking into account the blurring boundary between diagnostics and research, and specific counseling options for exome- and genome-based diagnostics. We conclude that alternative diagnoses may infer a certain level of 'greediness' to come to a positive diagnosis in interpreting sequencing results. Moreover, there is an increasing interdependence of clinic, diagnostics and research departments for comprehensive diagnostic genome care. Therefore, we invite clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care

Evidence for SMAD3 as a modifier of breast cancer risk in BRCA2 mutation carriers

Abstract Introduction Current attempts to identify genetic modifiers of BRCA1 and BRCA2 associated risk have focused on a candidate gene approach, based on knowledge of gene functions, or the development of large genome-wide association studies. In this study, we evaluated 24 SNPs tagged to 14 candidate genes derived through a novel approach that analysed gene expression differences to prioritise candidate modifier genes for association studies. Methods We successfully genotyped 24 SNPs in a cohort of up to 4,724 BRCA1 and 2,693 BRCA2 female mutation carriers from 15 study groups and assessed whether these variants were associated with risk of breast cancer in BRCA1 and BRCA2 mutation carriers. Results SNPs in five of the 14 candidate genes showed evidence of association with breast cancer risk for BRCA1 or BRCA2 carriers (P < 0.05). Notably, the minor alleles of two SNPs (rs7166081 and rs3825977) in high linkage disequilibrium (r 2 = 0.77), located at the SMAD3 locus (15q22), were each associated with increased breast cancer risk for BRCA2 mutation carriers (relative risk = 1.25, 95% confidence interval = 1.07 to 1.45, P trend = 0.004; and relative risk = 1.20, 95% confidence interval = 1.03 to 1.40, P trend = 0.018). Conclusions This study provides evidence that the SMAD3 gene, which encodes a key regulatory protein in the transforming growth factor beta signalling pathway and is known to interact directly with BRCA2, may contribute to increased risk of breast cancer in BRCA2 mutation carriers. This finding suggests that genes with expression associated with BRCA1 and BRCA2 mutation status are enriched for the presence of common genetic modifiers of breast cancer risk in these populations

Growth and Self-Assembly of CsPbBr3 Nanocrystals in the TOPO/PbBr2 Synthesis as Seen with X-ray Scattering

Despite broad interest in colloidal lead halide perovskite nanocrystals (LHP NCs), their intrinsic fast growth has prevented controlled synthesis of small, monodisperse crystals and insights into the reaction mechanism. Recently, a much slower synthesis of LHP NCs with extreme size control has been reported, based on diluted TOPO/PbBr2 precursors and a diisooctylphosphinate capping ligand. We report new insights into the nucleation, growth, and self-assembly in this reaction, obtained by in situ synchrotron-based small-angle X-ray scattering and optical absorption spectroscopy. We show that dispersed 3 nm Cs[PbBr3] agglomerates are the key intermediate species: first, they slowly nucleate into crystals, and then they release Cs[PbBr3] monomers for further growth of the crystals. We show the merits of a low Cs[PbBr3] monomer concentration for the reaction based on oleate ligands. We also examine the spontaneous superlattice formation mechanism occurring when the growing nanocrystals in the solvent reach a critical size of 11.6 nm.ISSN:1530-6984ISSN:1530-699

Growth and Self-Assembly of CsPbBr3_3 Nanocrystals in the TOPO/PbBr2_2 Synthesis as Seen with X-ray Scattering

Despite broad interest in colloidal lead halide perovskite nanocrystals (LHP NCs), their intrinsic fast growth has prevented controlled synthesis of small, monodisperse crystals and insights into the reaction mechanism. Recently, a much slower synthesis of LHP NCs with extreme size control has been reported, based on diluted TOPO/PbBr$_2$ precursors and a diisooctylphosphinate capping ligand. We report new insights into the nucleation, growth, and self-assembly in this reaction, obtained by in situ synchrotron-based small-angle X-ray scattering and optical absorption spectroscopy. We show that dispersed 3 nm Cs[PbBr$_3$] agglomerates are the key intermediate species: first, they slowly nucleate into crystals, and then they release Cs[PbBr$_3$] monomers for further growth of the crystals. We show the merits of a low Cs[PbBr$_3$] monomer concentration for the reaction based on oleate ligands. We also examine the spontaneous superlattice formation mechanism occurring when the growing nanocrystals in the solvent reach a critical size of 11.6 nm

Радиационная стойкость нитевидных кристаллов SiGe, используемых для сенсоров физических величин

Приведены результаты исследования влияния облучения γ-квантами дозами до 1·10¹⁸ см⁻² и магнитного поля с индукцией до 14 Тл на электропроводность нитевидных кристаллов Si1-xGex в интервале температуры 4,2-300 К.Вивчено вплив опромінення γ-квантами (випромінювання Co⁶⁰) з дозами до 1·10¹⁸ см⁻² та магнітного поля з індукцією до 14 Тл на електропровідність ниткоподібних кристалів Si1-xGex (х = 0,03) з питомим опором 0,08,0,025 Ом·см в інтервалі температур 4,2 .300 К. Встановлено, що опір кристалів слабо змінюється в процесі опромінення дозами до 2·10¹⁷ см⁻², в той же час спостерігаються істотні зміни магнітоопору. На основі проведених досліджень запропоновано умови створення радіаційно стійких сенсорів деформації, дієздатних в умовах сильних магнітних полів.An influence of γ-irradiation (Co⁶⁰) with doze up to 1·10¹⁸ cm⁻² and magnetic field with induction up to 14 T on conduction of Si1-xGex (x = 0,03) whisker crystals with resistivity of 0,08-0,025 Ohm·cm in temperature range 4,2-300 K have been studied. It is shown that whisker crystals resistance faintly varies under irradiation with doze 2·10¹⁷ cm⁻², while their magnetoresistance substantially changes. The strain sensors stable to irradiation action operating in high magnetic fields on the base of the whiskers have been designed

Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers

Two single nucleotide polymorphisms (SNPs) at 6q25.1, near the ESR1 gene, have been implicated in the susceptibility to breast cancer for Asian (rs2046210) and European women (rs9397435). A genome-wide association study in Europeans identified two further breast cancer susceptibility variants: rs11249433 at 1p11.2 and rs999737 in RAD51L1 at 14q24.1. Although previously identified breast cancer susceptibility variants have been shown to be associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers, the involvement of these SNPs to breast cancer susceptibility in mutation carriers is currently unknown. To address this, we genotyped these SNPs in BRCA1 and BRCA2 mutation carriers from 42 studies from the Consortium of Investigators of Modifiers of BRCA1/2. In the analysis of 14 123 BRCA1 and 8053 BRCA2 mutation carriers of European ancestry, the 6q25.1 SNPs (r2= 0.14) were independently associated with the risk of breast cancer for BRCA1 mutation carriers [hazard ratio (HR) = 1.17, 95% confidence interval (CI): 1.11-1.23, P-trend = 4.5 × 10-9for rs2046210; HR = 1.28, 95% CI: 1.18-1.40, P-trend = 1.3 × 10-8for rs9397435], but only rs9397435 was associated with the risk for BRCA2 carriers (HR = 1.14, 95% CI: 1.01-1.28, P-trend = 0.031). SNP rs11249433 (1p11.2) was associated with the risk of breast cancer for BRCA2 mutation carriers (HR = 1.09, 95% CI: 1.02-1.17, P-trend = 0.015), but was not associated with breast cancer risk for BRCA1 mutation carriers (HR = 0.97, 95% CI: 0.92-1.02, P-trend = 0.20). SNP rs999737 (RAD51L1) was not associated with breast cancer risk for either BRCA1 or BRCA2 mutation carriers (P-trend = 0.27 and 0.30, respectively). The identification of SNPs at 6q25.1 associated with breast cancer risk for BRCA1 mutation carriers will lead to a better understanding of the biology of tumour development in these women