Recent advances in DNA sequencing have enabled mapping of genes for monogenic traits in families with small pedigrees and even in unrelated cases. We report the identification of disease-causing ...mutations in a rare, severe, skeletal dysplasia, studying a family of two healthy unrelated parents and two affected children using whole-exome sequencing. The two affected daughters have clinical and radiographic features suggestive of anauxetic dysplasia (OMIM 607095), a rare form of dwarfism caused by mutations of RMRP. However, mutations of RMRP were excluded in this family by direct sequencing. Our studies identified two novel compound heterozygous loss-of-function mutations in POP1, which encodes a core component of the RNase mitochondrial RNA processing (RNase MRP) complex that directly interacts with the RMRP RNA domains that are affected in anauxetic dysplasia. We demonstrate that these mutations impair the integrity and activity of this complex and that they impair cell proliferation, providing likely molecular and cellular mechanisms by which POP1 mutations cause this severe skeletal dysplasia.
Abstract 1690
Acute Myeloid Leukaemia (AML) has a worldwide incidence of approximately 3.5 per 100,000 population per year with most cases occurring in adults. Survival at 12 months is less than 30% ...and at 5 years is less than 10% (NCI, 2010). AML is a complex disease that demonstrates marked heterogeneity morphologically, cytogenetically and molecularly. The largest cytogenetic subgroup of AML has normal cytogenetics and accounts for approximately 45% of de novo AML cases. Furthermore, the response to treatment and survival outcomes of cytogenetically normal AML (cn-AML) is remarkably heterogeneous.
– To undertake whole-genome and exome sequence analysis of a cn-AML case at diagnosis and at relapse to identify subtle, potentially oncogenic mutations at the molecular level that may initiate AML and those that may be responsible for drug resistance or relapse.
i. –Comparison of the AML genomes at diagnosis, remission and relapse to identify genomic regions with changes in copy number and loss of heterozygosity, using single nucleotide polymorphism (SNP) microarray analysis. ii. Identify chromosomal rearrangements such as small insertions, duplications, inversions and deletions, (“indels”) and translocations that may contribute to AML initiation or relapse, using massively parallel, ultra-high throughput (“next generation”), paired-end sequencing of total genomic DNA at low depth. iii. Identify DNA point mutations potentially affecting protein function that may contribute to AML initiation or relapse by using next generation sequencing at high depth of the captured exomes (putative coding regions) of the AML and control genomes.
The PwC (Price-Waterhouse-Coopers) Leukaemia and Lymphoma Tissue Bank, a joint initiative of the Australasian Leukaemia and Lymphoma Group and the Leukaemia Foundation, provided samples from an AML patient with normal cytogenetics and a blast count at diagnosis of 70% and at relapse of 85%. Genomic DNA extracted from autologous mesenchymal stem/stromal cells (MSCs) was used to represent non-leukaemic, germline, control DNA. Primary cell culture of MSCs from cryopreserved bone marrow aspirate cells (50 × 106) of our test patient at remission was achieved with standard tissue culture methods. High molecular weight DNA was extracted from the patient's MSCs and marrow cells at diagnosis, remission and relapse samples. Sonication (Covaris) and libraries appropriate for paired-end high-throughput sequencing (Illumina Genome Analyzer II instrument) were prepared from gel purified DNA fragments approximately 200 bp in size.
Primary cell culture of MSCs from bone marrow aspirates proved to be a robust source of germline genomic DNA with several advantages over skin. Firstly, tissue banked samples, will not include biopsies of normal skin. Furthermore, skin can be contaminated by circulating leukaemic cells, which is problematic with low-depth genomic sequencing. The homogenous immunophenotype of the cultured MSCs indicate their purity. Preliminary SNP microarray analysis identified a large region of uniparental disomy (copy number neutral loss of heterozygosity) involving most of chromosome 13q, which was not identified by standard cytogenetic analysis. Low-pass or shallow paired-end genomic DNA sequencing has generated the following outputs. MSC genome: 10.7 Gb (3.6X haploid genome coverage) resulting from 152 × 106 paired sequence reads, AML_diagnosis genome: 21.6 Gb (7.2X) resulting from 142 × 106 paired sequence reads, AML_relapse genome: 26.8 Gb (8.9X) resulting from 177 × 106 paired sequence reads. The capture baits representing the human exome span 26,225,870 bp (approximately 0.9% of haploid human genome). Exome capture libraries were prepared from the three sources of DNA (MSC, AML_diagnosis and AML_relapse) and sequenced using a single lane for each library. The outputs for all three were very similar, approximately 23 × 106 paired sequence reads, representing 1.3 Gb (49X haploid exome coverage). The reads for whole genome or exome capture were of high quality and more than 98% could be unambiguously aligned to the human reference genome in the correct orientation and interval distance. Here we will present MSC enrichment results and sequencing output results, quality control and preliminary analysis of genomic alterations and exonic mutations.
No relevant conflicts of interest to declare.
Objective
Ankylosing spondylitis (AS) is a highly heritable common inflammatory arthritis that targets the spine and sacroiliac joints of the pelvis, causing pain and stiffness and leading eventually ...to joint fusion. Although previous studies have shown a strong association of IL23R with AS in white Europeans, similar studies in East Asian populations have shown no association with common variants of IL23R, suggesting either that IL23R variants have no role or that rare genetic variants contribute. The present study was undertaken to screen IL23R to identify rare variants associated with AS in Han Chinese.
Methods
A 170‐kb region containing IL23R and its flanking regions was sequenced in 50 patients with AS and 50 ethnically matched healthy control subjects from a Han Chinese population. In addition, the 30‐kb region of peak association in white Europeans was sequenced in 650 patients with AS and 1,300 healthy controls. Validation genotyping was undertaken in 846 patients with AS and 1,308 healthy controls.
Results
We identified 1,047 variants, of which 729 were not found in the dbSNP genomic build 130. Several potentially functional rare variants in IL23R were identified, including one nonsynonomous single‐nucleotide polymorphism (nsSNP), Gly149Arg (position 67421184 GA on chromosome 1). Validation genotyping showed that the Gly149Arg variant was associated with AS (odds ratio 0.61, P = 0.0054).
Conclusion
This is the first study to implicate rare IL23R variants in the pathogenesis of AS. The results identified a low‐frequency nsSNP with predicted loss‐of‐function effects that was protectively associated with AS in Han Chinese, suggesting that decreased function of the interleukin‐23 (IL‐23) receptor protects against AS. These findings further support the notion that IL‐23 signaling has an important role in the pathogenesis of AS.
The outstanding optical quality of lead halide perovskites inspires studies of their potential for the optical control of carrier spins as pursued in other materials. Entering largely uncharted ...territory, time‐resolved pump–probe Kerr rotation is used to explore the coherent spin dynamics of electrons and holes in bulk formamidinium caesium lead iodine bromide (FA0.9Cs0.1PbI2.8Br0.2) and to determine key parameters characterizing interactions of their spins, such as the g‐factors and relaxation times. The demonstrated long spin dynamics and narrow g‐factor distribution prove the perovskites as promising competitors for conventional semiconductors in spintronics. The dynamic nuclear polarization via spin‐oriented holes is realized and the identification of the lead (207Pb) isotope in optically detected nuclear magnetic resonance proves that the hole–nuclei interaction is dominated by the lead ions. A detailed theoretical analysis accounting for the specifics of the lead halide perovskite materials allows the evaluation of the underlying hyperfine interaction constants, both for electrons and holes. Recombination and spin dynamics evidence that at low temperatures, photogenerated electrons and holes are localized at different regions of the perovskite crystal, resulting in their long lifetimes up to 44 μs. The findings form the base for the tailored development of spin‐optoelectronic applications for the large family of lead halide perovskites and their nanostructures.
Building up on the excellent optical properties of perovskite materials, the electron and hole spin dynamics provide fundamental insights into the carrier–nuclear spin system. In the model perovskite, bulk FA0.9Cs0.1PbI2.8Br0.2, Landé factors, key spin relaxation times, and mechanisms are determined. Optically detected NMR reveals the dominance of the lead spin hyperfine interaction at the top of the valence band.
The tunability of the optical properties of lead halide perovskite nanocrystals makes them highly appealing for applications. Halide anion exchange and quantum confinement enable tailoring of the ...band gap. For spintronics, the Landé g-factors of electrons and holes are essential. Using empirical tight-binding and k·p methods, we calculate them for nanocrystals of all-inorganic lead halide perovskites CsPbX 3 (X = I, Br, Cl). The hole g-factor band gap dependence follows the universal law found for bulk perovskites, while for electrons, a considerable modification is predicted. Based on the k·p analysis, we conclude that this difference arises from the interaction of the bottom conduction band with the spin–orbit split electron states. These predictions are confirmed experimentally for electron and hole g-factors in CsPbI3 nanocrystals in a glass matrix, measured by time-resolved Faraday ellipticity in a magnetic field at cryogenic temperatures.
Abstract Quantum technologic and spintronic applications require reliable material platforms that enable significant and long‐living spin polarization of excitations, the ability to manipulate it ...optically in external fields, and the possibility to implement quantum correlations between spins, i.e., entanglement. Here it is demonstrated that these conditions are met in bulk crystals of lead halide perovskites. A giant optical orientation of 85% of excitons, approaching the ultimate limit of unity, in FA 0.9 Cs 0.1 PbI 2.8 Br 0.2 crystals is reported. The exciton spin orientation is maintained during the exciton lifetime of 55 ps resulting in high circular polarization of the exciton emission. The optical orientation is robust to detuning of the excitation energy up to 0.3 eV above the exciton resonance and remains larger than 20% up to detunings of 0.9 eV. It evidences pure chiral selection rules and suppressed spin relaxation of electrons and holes, even with large kinetic energies. The exciton and electron–hole recombinations are distinguished by means of the spin dynamics detected via coherent spin quantum beats in magnetic field. Further, electron–hole spin correlations are demonstrated through linear polarization beats after circularly polarized excitation. These findings are supported by atomistic calculations. All‐in‐all, the results establish lead halide perovskite semiconductors as suitable platform for quantum technologies.
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