SNP arrays to confirm X-linkage in a family with idiopathic intellectual disability
ABSTRACT: L061 family with idiopathic non-syndromic intellectual disability remained unsolved after targeted screening of ID-related genes, array-CGH and exome sequencing. In order to perform custom tandem repeat screening on the X chromosome by long read single molecule sequencing, X-linkage needed to be confirmed by SNP arrays.
BACKGROUND:The etiology of more than half of all patients with X-linked intellectual disability remains elusive, despite array-based comparative genomic hybridization, whole exome or genome sequencing. Since short read massive parallel sequencing approaches do not allow the detection of larger tandem repeat expansions, we hypothesized that such expansions could be a hidden cause of X-linked intellectual disability. METHODS:We selectively captured over 1800 tandem repeats on the X chromosome and ...[more]
Project description:Epigenetic mechanisms including histone modifications have emerged as important factors influencing cell fate determination. The functional role of H3K4 methylation, however, remains largely unclear in the maintenance and differentiation of hematopoietic stem/progenitor cells (HSC/HPCs). Here we show that DPY30, a shared core subunit of the SET1/MLL family methyltransferase complexes and a facilitator of their H3K4 methylation activity, is important for ex vivo proliferation and differentiation of human CD34+ HPCs. DPY30 promotes HPC proliferation by directly regulating the expression of genes critical for cell proliferation. Interestingly, while DPY30 knockdown (KD) in HPCs impaired their differentiation into the myelomonocytic lineage, it potently promoted hemoglobin production and affected the kinetics of their differentiation into the erythroid lineage. In an in vivo model, we show that morpholino-mediated dpy30 KD resulted in severe defects in the development of the zebrafish hematopoietic system, which could be partially rescued by co-injection of dpy30 mRNA. Taken together, our results establish a critical role of DPY30 in the proliferation and appropriate differentiation of hematopoietic progenitor cells as well as in animal hematopoiesis. Finally, we also demonstrate a crucial role of DPY30 in the growth of several MLL1-fusion-mediated leukemia cell lines. Total RNAs from control (scr) or knockdown (hD2, hD5) cells before and after culturing under condition promoting myelomonocytic differentiation were subjected to Illumina microarray analyses.
Project description:Large scale analysis of balanced chromosomal translocation breakpoints has shown nonhomologous end joining and microhomology-mediated repair to be the main drivers of interchromosomal structural aberrations. Breakpoint sequences of de novo unbalanced translocations have not yet been investigated systematically. We analyzed 12 de novo translocations and mapped the breakpoints in 9. Surprisingly, in contrast to balanced translocations, we identify non-allelic homologous recombination (NAHR) between (retro)transposable elements and especially long interspersed elements (LINEs) as the main mutational mechanism. This finding implicates (retro)transposons to be a major driver of genomic rearrangements and exposes a profoundly different mutational mechanism compared to balanced chromosomal translocations. Furthermore, we show the existence of compound maternal/paternal derivative chromosomes, reinforcing the hypothesis that human cleavage stage embryogenesis is a cradle of chromosomal rearrangements. In total 36 non-amplified genomic DNA samples (12 patients plus parents) extracted from blood or amniocytes were analyzed by 250K Nsp I SNP arrays (GEO accession number GPL3718).
Project description:The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and analysis issues. We demonstrate the consistency of results within a platform across test sites as well as the high level of cross-platform concordance in terms of genes identified as differentially expressed. The MAQC study provides a rich resource that will help build consensus on the use of microarrays in research, clinical and regulatory settings. Manuscripts related to the MAQC project have been published in Nature Biotechnology, 24(9), September, 2006. More information about the MAQC project can be found at http://edkb.fda.gov/MAQC/.<br><br>Expression data from two distinct reference RNA samples (A and B) in four titration pools were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Sample A = Stratagene Universal Human Reference RNA (UHRR, Catalog #740000), Sample B = Ambion Human Brain Reference RNA (HBRR, Catalog #6050), Sample C = Samples A and B mixed at 75%:25% ratio (A:B); and Sample D = Samples A and B mixed at 25%:75% ratio (A:B). In general, each microarray platform was tested at three sites and each sample was tested in five replicates at each test site. Samples (hybridizations) were named according to the following convention: Platform_Testsite_SampleRelicate. For example, AFX_2_B1 represents the hybridization (array) from platform AFX processed by test site 2 for the first replicate of sample B. Assignment of platform code: ABI = Applied Biosystems (microarray); AFX = Affymetrix; AG1 = Agilent one-color; AGL = Agilent two-color; GEH = GE Healthcare; ILM = Illumina; NCI = NCI two-color (Operon oligos); EPP = Eppendorf; TAQ = TaqMan (Applied Biosystems); QGN = QuantiGene (Panomics); GEX = StaRT-PCR (Gene Express); H25K = TeleChem two-color; H25K1 = TeleChem one-color; BIO = CapitalBio two-color (Operon oligos); BIO1 = CapitalBio one-color (Operon oligos); OPN = Operon two-color (Operon oligos); NMC = Norwegian Microarray Consortium two-color (Operon oligos).
Project description:Here, using LC-MS/MS, we describe for the first time a linkage region trisaccharide comprising [-GlcUA-Gal-Xyl-O-] as an alternative point of entry for glycosaminoglycan (GAG) biosynthesis. The trisaccharide was identified in the proteoglycan bikunin from urine of human healthy donors present as a disulfated pentasaccharide, [deltaHexUA-GalNAc(S)-GlcUA-Gal(S)-Xyl-O-] after chondroitinase ABC degradation. Furthermore, it was identified in chondroitin sulfate primed on xylosides isolated from human cell lines, present as the corresponding disulfated pentasaccharide after chondroitinase ABC degradation.
Project description:This array is designed to compare the differentially expressed genes in control mouse skin and keratinocytes-specific N-WASP knockout mouse skin (k5 cre). Ext-01 file is the array analysis from backskin of control mouse and Ext-02 file is the array analysis from backskin of N-WASP ko mouse.