Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome.

Abstract:

:We have explored the National Center for Biotechnology Information (NCBI) single nucleotide polymorphisms (SNPs) database for a correlation between the density of putative SNPs, as well as SNPs that map to different chromosomal locations (ambiguously mapped SNPs), and segmental duplications of DNA in chromosome regions involved in genomic disorders. A high density of SNPs (14.4 and 12.4 SNPs per kb) was detected in the low copy repeats (LCRs) responsible for the chromosome 17p12 duplication and deletion that cause peripheral neuropathies. None of the SNPs at the PMP22 gene were ambiguously mapped, but 93% of the SNPs at LCRs mapped on both LCR copies, indicating that they are in fact variants in paralogous sequences. Similarly, a high SNP density was found in the LCR regions flanking the neurofibromatosis type 1 (NF1) gene, with 80% of SNPs mapping on both LCR copies. A high density of SNPs was found within LCR sequences involved in the deletions that mediate contiguous gene syndromes on chromosomes 7q11, 15q11-q13 and 22q11. We have analyzed the whole sequence of chromosome 22, which contains 14% of ambiguously mapped SNPs, and have found a good correlation between these SNPs and segmental duplications detected by BLAST analysis. We have identified several segments of ambiguously mapped SNPs, four corresponding to LCRs involved in the chromosome 22q11 microdeletion syndromes. Our data indicate that most SNPs in LCR segments are in fact paralogous sequence variants (PSVs), and suggest that a significant proportion of the SNPs in the NCBI database correspond to PSVs within segmental duplications of the human genome sequence.

journal_name

Hum Mol Genet

journal_title

Human molecular genetics

authors

Estivill X,Cheung J,Pujana MA,Nakabayashi K,Scherer SW,Tsui LC

doi

10.1093/hmg/11.17.1987

subject

Has Abstract

pub_date

2002-08-15 00:00:00

pages

1987-95

issue

17

eissn

0964-6906

issn

1460-2083

journal_volume

11

pub_type

杂志文章
  • Generalized metabolic bone disease and fracture risk in Rothmund-Thomson syndrome.

    abstract::Rothmund-Thomson syndrome (RTS) is a rare autosomal recessive disorder characterized by poikiloderma, small stature, sparse hair, skeletal abnormalities, increased risk of osteosarcoma, and decreased bone mass. To date, there has not been a comprehensive evaluation of the prevalence and extent of metabolic bone diseas...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx178

    authors: Cao F,Lu L,Abrams SA,Hawthorne KM,Tam A,Jin W,Dawson B,Shypailo R,Liu H,Lee B,Nagamani SCS,Wang LL

    更新日期:2017-08-15 00:00:00

  • Unequal interchromosomal rearrangements may result in elastin gene deletions causing the Williams-Beuren syndrome.

    abstract::Williams-Beuren syndrome (WBS) is generally the consequence of an interstitial microdeletion at 7q11.23, which includes the elastin gene, thus causing hemizygosity at the elastin gene locus. The origin of the deletion has been reported by many authors to be maternal in approximately 60% and paternal in 40% of cases. S...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.12.1893

    authors: Dutly F,Schinzel A

    更新日期:1996-12-01 00:00:00

  • Rapid identification of gene sequences for transcriptional map assembly by direct cDNA screening of genomic reference libraries.

    abstract::We have used the direct cDNA screening protocol to identify sequences transcribed in cerebral cortex from a reference library of human Xq28. To derive coding sequences from these genomic clones, we first identified fragments containing transcribed sequences and subjected these to exon trapping or to partial sequencing...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/3.11.2019

    authors: Lawrence BJ,Schwabe W,Kioschis P,Coy JF,Poustka A,Brennan MB,Hochgeschwender U

    更新日期:1994-11-01 00:00:00

  • Parkin functionally interacts with PGC-1α to preserve mitochondria and protect dopaminergic neurons.

    abstract::To understand the cause of Parkinson's disease (PD), it is important to determine the functional interactions between factors linked to the disease. Parkin is associated with autosomal recessive early-onset PD, and controls the transcription of PGC-1α, a master regulator of mitochondrial biogenesis. These two factors ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw418

    authors: Zheng L,Bernard-Marissal N,Moullan N,D'Amico D,Auwerx J,Moore DJ,Knott G,Aebischer P,Schneider BL

    更新日期:2017-02-01 00:00:00

  • Mouse models of X-linked juvenile retinoschisis have an early onset phenotype, the severity of which varies with genotype.

    abstract::X-linked juvenile retinoschisis (XLRS) is an early-onset inherited condition that affects primarily males and is characterized by cystic lesions of the inner retina, decreased visual acuity and contrast sensitivity and a selective reduction of the electroretinogram (ERG) b-wave. Although XLRS is genetically heterogene...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz122

    authors: Liu Y,Kinoshita J,Ivanova E,Sun D,Li H,Liao T,Cao J,Bell BA,Wang JM,Tang Y,Brydges S,Peachey NS,Sagdullaev BT,Romano C

    更新日期:2019-09-15 00:00:00

  • Protein kinase C gamma, a protein causative for dominant ataxia, negatively regulates nuclear import of recessive-ataxia-related aprataxin.

    abstract::Spinocerebellar ataxia type 14 (SCA14) is an autosomal dominant disease caused by mutations in the gene encoding protein kinase C gamma (PKC gamma). We report an SCA14 family with a novel deletion of a termination-codon-containing region, resulting in a missense change and a C-terminal 13-amino-acid extension with inc...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddp298

    authors: Asai H,Hirano M,Shimada K,Kiriyama T,Furiya Y,Ikeda M,Iwamoto T,Mori T,Nishinaka K,Konishi N,Udaka F,Ueno S

    更新日期:2009-10-01 00:00:00

  • Worldwide distribution and broader clinical spectrum of muscle-eye-brain disease.

    abstract::Muscle-eye-brain disease (MEB), an autosomal recessive disorder prevalent in Finland, is characterized by congenital muscular dystrophy, brain malformation and ocular abnormalities. Since the MEB phenotype overlaps substantially with those of Fukuyama-type congenital muscular dystrophy (FCMD) and Walker-Warburg syndro...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddg043

    authors: Taniguchi K,Kobayashi K,Saito K,Yamanouchi H,Ohnuma A,Hayashi YK,Manya H,Jin DK,Lee M,Parano E,Falsaperla R,Pavone P,Van Coster R,Talim B,Steinbrecher A,Straub V,Nishino I,Topaloglu H,Voit T,Endo T,Toda T

    更新日期:2003-03-01 00:00:00

  • Duplication of Glu37 in the switch I region of HRAS impairs effector/GAP binding and underlies Costello syndrome by promoting enhanced growth factor-dependent MAPK and AKT activation.

    abstract::Costello syndrome (CS) is a developmental disorder characterized by postnatal reduced growth, facial dysmorphism, cardiac defects, mental retardation and skin and musculo-skeletal defects. CS is caused by HRAS germline mutations. In the majority of cases, mutations affect Gly(12) and Gly(13) and are associated with a ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddp548

    authors: Gremer L,De Luca A,Merbitz-Zahradnik T,Dallapiccola B,Morlot S,Tartaglia M,Kutsche K,Ahmadian MR,Rosenberger G

    更新日期:2010-03-01 00:00:00

  • Ultra-sensitive FISH using peroxidase-mediated deposition of biotin- or fluorochrome tyramides.

    abstract::We describe a detection principle for indirect fluorescence in situ hybridization (FISH) methods that with only one or two antibody layers dramatically improves FISH signal intensities. The method uses as a first layer an anti-hapten immunoglobulin [or (strept)avidin] conjugated to peroxidase. The quintessence of the ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/4.4.529

    authors: Raap AK,van de Corput MP,Vervenne RA,van Gijlswijk RP,Tanke HJ,Wiegant J

    更新日期:1995-04-01 00:00:00

  • Phosphorylation of parkin by Parkinson disease-linked kinase PINK1 activates parkin E3 ligase function and NF-kappaB signaling.

    abstract::Mutations in PTEN-induced putative kinase 1 (PINK1) or parkin cause autosomal recessive forms of Parkinson disease (PD), but how these mutations trigger neurodegeneration is poorly understood and the exact functional relationship between PINK1 and parkin remains unclear. Here, we report that PINK1 regulates the E3 ubi...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddp501

    authors: Sha D,Chin LS,Li L

    更新日期:2010-01-15 00:00:00

  • Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1.

    abstract::Genome-wide association studies of colorectal cancer (CRC) have identified a number of common variants associated with modest risk, including rs3802842 at chromosome 11q23.1. Several genes map to this region but rs3802842 does not map to any known transcribed or regulatory sequences. We reasoned, therefore, that rs380...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt584

    authors: Biancolella M,Fortini BK,Tring S,Plummer SJ,Mendoza-Fandino GA,Hartiala J,Hitchler MJ,Yan C,Schumacher FR,Conti DV,Edlund CK,Noushmehr H,Coetzee SG,Bresalier RS,Ahnen DJ,Barry EL,Berman BP,Rice JC,Coetzee GA,Casey G

    更新日期:2014-04-15 00:00:00

  • Mutations in congenital myasthenic syndromes reveal an epsilon subunit C-terminal cysteine, C470, crucial for maturation and surface expression of adult AChR.

    abstract::Many congenital myasthenic syndromes (CMS) are associated with mutations in the genes encoding the acetylcholine receptor (AChR), an oligomeric protein with the structure alpha(2)betadelta epsilon. AChR deficiency is frequently due to homozygous or heteroallelic mutations in the AChR epsilon subunit, most of which cau...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/11.24.3087

    authors: Ealing J,Webster R,Brownlow S,Abdelgany A,Oosterhuis H,Muntoni F,Vaux DJ,Vincent A,Beeson D

    更新日期:2002-11-15 00:00:00

  • De novo mutation in the COL4A5 gene converting glycine 325 to glutamic acid in Alport syndrome.

    abstract::Southern blot analysis of the COL4A5 gene in a 6 year old Italian Alport patient (proband VIZ) showed the loss of an MspI site that was present in the mother and control DNAs. PCR amplification and DNA sequencing revealed a single G-->A nucleotide change. The mutation results in substitution of a glutamic acid for a g...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/1.2.127

    authors: Renieri A,Seri M,Myers JC,Pihlajaniemi T,Massella L,Rizzoni G,De Marchi M

    更新日期:1992-05-01 00:00:00

  • Disruption of scribble (Scrb1) causes severe neural tube defects in the circletail mouse.

    abstract::Circletail is one of only two mouse mutants that exhibit the most severe form of neural tube defect (NTD), termed craniorachischisis. In this disorder, almost the entire brain and spinal cord is affected, owing to a failure to initiate neural tube closure. Craniorachischisis is a significant cause of lethality in huma...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddg014

    authors: Murdoch JN,Henderson DJ,Doudney K,Gaston-Massuet C,Phillips HM,Paternotte C,Arkell R,Stanier P,Copp AJ

    更新日期:2003-01-15 00:00:00

  • Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly.

    abstract::We report two siblings with infantile onset seizures, severe developmental delay and spastic paraplegia, in whom whole-genome sequencing revealed compound heterozygous mutations in the AP4S1 gene, encoding the σ subunit of the adaptor protein complex 4 (AP-4). The effect of the predicted loss-of-function variants (p.G...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu740

    authors: Hardies K,May P,Djémié T,Tarta-Arsene O,Deconinck T,Craiu D,AR working group of the EuroEPINOMICS RES Consortium.,Helbig I,Suls A,Balling R,Weckhuysen S,De Jonghe P,Hirst J

    更新日期:2015-04-15 00:00:00

  • Mutations in the accessory subunit NDUFB10 result in isolated complex I deficiency and illustrate the critical role of intermembrane space import for complex I holoenzyme assembly.

    abstract::An infant presented with fatal infantile lactic acidosis and cardiomyopathy, and was found to have profoundly decreased activity of respiratory chain complex I in muscle, heart and liver. Exome sequencing revealed compound heterozygous mutations in NDUFB10, which encodes an accessory subunit located within the PD part...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw431

    authors: Friederich MW,Erdogan AJ,Coughlin CR 2nd,Elos MT,Jiang H,O'Rourke CP,Lovell MA,Wartchow E,Gowan K,Chatfield KC,Chick WS,Spector EB,Van Hove JLK,Riemer J

    更新日期:2017-02-15 00:00:00

  • Satellite cell loss and impaired muscle regeneration in selenoprotein N deficiency.

    abstract::Selenoprotein N (SelN) deficiency causes a group of inherited neuromuscular disorders termed SEPN1-related myopathies (SEPN1-RM). Although the function of SelN remains unknown, recent data demonstrated that it is dispensable for mouse embryogenesis and suggested its involvement in the regulation of ryanodine receptors...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq515

    authors: Castets P,Bertrand AT,Beuvin M,Ferry A,Le Grand F,Castets M,Chazot G,Rederstorff M,Krol A,Lescure A,Romero NB,Guicheney P,Allamand V

    更新日期:2011-02-15 00:00:00

  • Usher syndromes due to MYO7A, PCDH15, USH2A or GPR98 mutations share retinal disease mechanism.

    abstract::Usher syndrome (USH) is a genetically heterogeneous group of autosomal recessive deaf-blinding disorders. Pathophysiology leading to the blinding retinal degeneration in USH is uncertain. There is evidence for involvement of the photoreceptor cilium, photoreceptor synapse, the adjacent retinal pigment epithelium (RPE)...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddn140

    authors: Jacobson SG,Cideciyan AV,Aleman TS,Sumaroka A,Roman AJ,Gardner LM,Prosser HM,Mishra M,Bech-Hansen NT,Herrera W,Schwartz SB,Liu XZ,Kimberling WJ,Steel KP,Williams DS

    更新日期:2008-08-01 00:00:00

  • Sonic Hedgehog, a key development gene, experienced intensified molecular evolution in primates.

    abstract::Sonic Hedgehog (SHH) is one of the most intensively studied genes in developmental biology. It is a highly conserved gene, found in species as diverse as arthropods and mammals. The mammalian SHH encodes a signaling molecule that plays a central role in developmental patterning, especially of the nervous system and th...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddl123

    authors: Dorus S,Anderson JR,Vallender EJ,Gilbert SL,Zhang L,Chemnick LG,Ryder OA,Li W,Lahn BT

    更新日期:2006-07-01 00:00:00

  • Meta-analysis of genome scans of age-related macular degeneration.

    abstract::A genetic contribution to the development of age-related macular degeneration (AMD) is well established. Several genome-wide linkage studies have identified a number of putative susceptibility loci for AMD but only a few of these regions have been replicated in independent studies. Here, we perform a meta-analysis of ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,meta分析

    doi:10.1093/hmg/ddi230

    authors: Fisher SA,Abecasis GR,Yashar BM,Zareparsi S,Swaroop A,Iyengar SK,Klein BE,Klein R,Lee KE,Majewski J,Schultz DW,Klein ML,Seddon JM,Santangelo SL,Weeks DE,Conley YP,Mah TS,Schmidt S,Haines JL,Pericak-Vance MA,Gorin

    更新日期:2005-08-01 00:00:00

  • Systemic transplantation of c-kit+ cells exerts a therapeutic effect in a model of amyotrophic lateral sclerosis.

    abstract::Amyotrophic lateral sclerosis (ALS) is a progressive, fatal, neurodegenerative disease characterized by the loss of motor neurons. Motor neuron degeneration is probably both a cell autonomous and a non-autonomous event. Therefore, manipulating the diseased microenvironment via non-neural cell replacement could be a th...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq293

    authors: Corti S,Nizzardo M,Nardini M,Donadoni C,Salani S,Simone C,Falcone M,Riboldi G,Govoni A,Bresolin N,Comi GP

    更新日期:2010-10-01 00:00:00

  • Involvement of the ubiquitin-proteasome pathway and molecular chaperones in oculopharyngeal muscular dystrophy.

    abstract::Oculopharyngeal muscular dystrophy (OPMD) is a late-onset autosomal dominant muscular dystrophy that results from small expansions of a polyalanine tract in the PABPN1 gene. Intranuclear inclusions are the pathological hallmark of OPMD. The mechanism by which protein aggregation in OPMD might relate to a toxic gain-of...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddg293

    authors: Abu-Baker A,Messaed C,Laganiere J,Gaspar C,Brais B,Rouleau GA

    更新日期:2003-10-15 00:00:00

  • Genome-wide expression profiling of lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways.

    abstract::Autism is a heterogeneous condition that is likely to result from the combined effects of multiple genetic factors interacting with environmental factors. Given its complexity, the study of autism associated with Mendelian single gene disorders or known chromosomal etiologies provides an important perspective. We used...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddm116

    authors: Nishimura Y,Martin CL,Vazquez-Lopez A,Spence SJ,Alvarez-Retuerto AI,Sigman M,Steindler C,Pellegrini S,Schanen NC,Warren ST,Geschwind DH

    更新日期:2007-07-15 00:00:00

  • Complete loss-of-function of the heart/muscle-specific adenine nucleotide translocator is associated with mitochondrial myopathy and cardiomyopathy.

    abstract::Multiple mitochondrial DNA deletions are associated with clinically heterogeneous disorders transmitted as mendelian traits. Dominant missense mutations were found in the gene encoding the heart and skeletal muscle-specific isoform of the adenine nucleotide translocator (ANT1) in families with autosomal dominant progr...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi341

    authors: Palmieri L,Alberio S,Pisano I,Lodi T,Meznaric-Petrusa M,Zidar J,Santoro A,Scarcia P,Fontanesi F,Lamantea E,Ferrero I,Zeviani M

    更新日期:2005-10-15 00:00:00

  • Modeling Cornelia de Lange syndrome in vitro and in vivo reveals a role for cohesin complex in neuronal survival and differentiation.

    abstract::Cornelia de Lange syndrome (CdLS), which is reported to affect ∼1 in 10 000 to 30 000 newborns, is a multisystem organ developmental disorder with relatively mild to severe effects. Among others, intellectual disability represents an important feature of this condition. CdLS can result from mutations in at least five ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddy329

    authors: Bottai D,Spreafico M,Pistocchi A,Fazio G,Adami R,Grazioli P,Canu A,Bragato C,Rigamonti S,Parodi C,Cazzaniga G,Biondi A,Cotelli F,Selicorni A,Massa V

    更新日期:2019-01-01 00:00:00

  • Strategies to prevent cleavage of the linker region between ligand-binding repeats 4 and 5 of the LDL receptor.

    abstract::A main strategy for lowering plasma low-density lipoprotein (LDL) cholesterol levels is to increase the number of cell-surface LDL receptors (LDLRs). This can be achieved by increasing the synthesis or preventing the degradation of the LDLR. One mechanism by which an LDLR becomes non-functional is enzymatic cleavage w...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz164

    authors: Strøm TB,Bjune K,Costa LTD,Leren TP

    更新日期:2019-11-15 00:00:00

  • Cell-specific localization of CFTR mRNA shows developmentally regulated expression in human fetal tissues.

    abstract::An improved understanding of the expression of the cystic fibrosis gene (CFTR) will assist our approach to preventing the organ damage caused by cystic fibrosis (CF). We have studied the expression of CFTR in human fetal tissues at different gestational ages using in situ hybridization to detect CFTR mRNA. CFTR was pr...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/2.3.219

    authors: Tizzano EF,Chitayat D,Buchwald M

    更新日期:1993-03-01 00:00:00

  • LRRK2 functions as a Wnt signaling scaffold, bridging cytosolic proteins and membrane-localized LRP6.

    abstract::Mutations in PARK8, encoding leucine-rich repeat kinase 2 (LRRK2), are a frequent cause of Parkinson's disease (PD). Nonetheless, the physiological role of LRRK2 remains unclear. Here, we demonstrate that LRRK2 participates in canonical Wnt signaling as a scaffold. LRRK2 interacts with key Wnt signaling proteins of th...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/dds342

    authors: Berwick DC,Harvey K

    更新日期:2012-11-15 00:00:00

  • Polymorphisms in the PON gene cluster are associated with Alzheimer disease.

    abstract::Paraoxonase is an arylesterase enzyme that is expressed in the liver and found in the circulation in association with apoA1 and the high-density lipoprotein, and prevents the accumulation of oxidized lipids in low-density lipoproteins in vitro. Common polymorphisms in genes encoding paraoxonase are established risk fa...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi428

    authors: Erlich PM,Lunetta KL,Cupples LA,Huyck M,Green RC,Baldwin CT,Farrer LA,MIRAGE Study Group.

    更新日期:2006-01-01 00:00:00

  • Drosophila FMRP participates in the DNA damage response by regulating G2/M cell cycle checkpoint and apoptosis.

    abstract::Fragile X syndrome, the most common form of inherited mental retardation, is caused by the loss of the fragile X mental retardation protein (FMRP). FMRP is a ubiquitously expressed, multi-domain RNA-binding protein, but its in vivo function remains poorly understood. Recent studies have shown that FMRP participates in...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/dds307

    authors: Liu W,Jiang F,Bi X,Zhang YQ

    更新日期:2012-11-01 00:00:00