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      De novo pathogenic variants in CHAMP1 are associated with global developmental delay, intellectual disability, and dysmorphic facial features

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          Abstract

          We identified five unrelated individuals with significant global developmental delay and intellectual disability (ID), dysmorphic facial features and frequent microcephaly, and de novo predicted loss-of-function variants in chromosome alignment maintaining phosphoprotein 1 ( CHAMP1). Our findings are consistent with recently reported de novo mutations in CHAMP1 in five other individuals with similar features. CHAMP1 is a zinc finger protein involved in kinetochore–microtubule attachment and is required for regulating the proper alignment of chromosomes during metaphase in mitosis. Mutations in CHAMP1 may affect cell division and hence brain development and function, resulting in developmental delay and ID.

          Most cited references11

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          De novo mutations in human genetic disease.

          New mutations have long been known to cause genetic disease, but their true contribution to the disease burden can only now be determined using family-based whole-genome or whole-exome sequencing approaches. In this Review we discuss recent findings suggesting that de novo mutations play a prominent part in rare and common forms of neurodevelopmental diseases, including intellectual disability, autism and schizophrenia. De novo mutations provide a mechanism by which early-onset reproductively lethal diseases remain frequent in the population. These mutations, although individually rare, may capture a significant part of the heritability for complex genetic diseases that is not detectable by genome-wide association studies.
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            Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

            Heng Li (2012)
            Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion (INDEL) calling, can also be achieved with unitigs. Results: To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of information of the input reads. SNPs and INDELs can be called by mapping the unitigs against a reference genome. By applying the method on 35-fold human resequencing data, we showed that in comparison to the standard pipeline, our approach yields similar accuracy for SNP calling and better results for INDEL calling. It has higher sensitivity than other de novo assembly based methods for variant calling. Our work suggests that variant calling with de novo assembly be a beneficial complement to the standard variant calling pipeline for whole-genome resequencing. In the methodological aspects, we proposed FMD-index for forward-backward extension of DNA sequences, a fast algorithm for finding all super-maximal exact matches and one-pass construction of unitigs from an FMD-index. Availability: http://github.com/lh3/fermi Contact: hengli@broadinstitute.org
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              Mitotic spindle (DIS)orientation and DISease: Cause or consequence?

              Correct alignment of the mitotic spindle during cell division is crucial for cell fate determination, tissue organization, and development. Mutations causing brain diseases and cancer in humans and mice have been associated with spindle orientation defects. These defects are thought to lead to an imbalance between symmetric and asymmetric divisions, causing reduced or excessive cell proliferation. However, most of these disease-linked genes encode proteins that carry out multiple cellular functions. Here, we discuss whether spindle orientation defects are the direct cause for these diseases, or just a correlative side effect.
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                Author and article information

                Journal
                Cold Spring Harb Mol Case Stud
                Cold Spring Harb Mol Case Stud
                cshmcs
                cshmcs
                cshmcs
                Cold Spring Harbor Molecular Case Studies
                Cold Spring Harbor Laboratory Press
                2373-2865
                2373-2873
                January 2016
                : 2
                : 1
                : a000661
                Affiliations
                [1 ]Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA;
                [2 ]GeneDx, Gaithersburg, Maryland 20877, USA;
                [3 ]Greenwood Genetic Center, Greenwood, South Carolina 29646, USA;
                [4 ]Boston Children's Hospital, Boston, Massachusetts 02115, USA;
                [5 ]Duke University Medical Center, Durham, North Carolina 27710, USA;
                [6 ]Arkansas Children's Hospital, Little Rock, Arkansas 72202, USA;
                [7 ]Divisions of Medical Genetics and Pediatrics, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA;
                [8 ]Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
                Author notes
                Corresponding author: wkc15@ 123456columbia.edu
                Article
                TanakaMCS000661
                10.1101/mcs.a000661
                4849844
                27148580
                8ffaa97e-1aaf-450d-bc96-d128975985f9
                © 2016 Tanaka et al.; Published by Cold Spring Harbor Laboratory Press

                This article is distributed under the terms of the Creative Commons Attribution-NonCommercial License, which permits reuse and redistribution, except for commercial purposes, provided that the original author and source are credited.

                History
                : 13 August 2015
                : 30 October 2015
                Page count
                Pages: 8
                Funding
                Funded by: Simons Foundation http://dx.doi.org/10.13039/100000893
                Categories
                Research Report

                congenital microcephaly,intellectual disability, severe,severe global developmental delay

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