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ABSTRACT: Potocki-Shaffer syndrome (PSS) is a rare disorder caused by haploinsufficiency of genes located on the proximal short arm of chromosome 11 (11p11.2p12). Classic features include biparietal foramina, multiple exostoses, profound hypotonia, dysmorphic features, and developmental delay/intellectual disability. Fewer than 40 individuals with PSS have been reported, with variable clinical presentations due in part to disparity in deletion sizes. We report on a boy who presented for initial evaluation at age 13 months because of a history of developmental delay, hypotonia, subtle dysmorphic features, and neurobehavioral abnormalities. SNP microarray analysis identified a 137 kb deletion at 11p11.2, which maps within the classically defined PSS interval. This deletion results in haploinsufficiency for all or portions of six OMIM genes: SLC35C1, CRY2, MAPK8IP1, PEX16, GYLTL1B, and PHF21A. Recently, translocations interrupting PHF21A have been associated with intellectual disability and craniofacial anomalies similar to those seen in PSS. The identification of this small deletion in a child with developmental delay and hypotonia provides further evidence for the genetic basis of developmental disability and identifies a critical region sufficient to cause hypotonia in this syndrome. Additionally, this case illustrates the utility of high resolution genomic approaches in correlating clinical phenotypes with specific genes in contiguous gene deletion syndromes. © 2012 Wiley Periodicals, Inc.
American Journal of Medical Genetics Part A 12/2012; · 2.39 Impact Factor
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ABSTRACT: There is considerable interest in the use of next-generation sequencing to help diagnose unidentified genetic conditions, but it is difficult to predict the success rate in a clinical setting that includes patients with a broad range of phenotypic presentations.
The authors present a pilot programme of whole-exome sequencing on 12 patients with unexplained and apparent genetic conditions, along with their unaffected parents. Unlike many previous studies, the authors did not seek patients with similar phenotypes, but rather enrolled any undiagnosed proband with an apparent genetic condition when predetermined criteria were met.
This undertaking resulted in a likely genetic diagnosis in 6 of the 12 probands, including the identification of apparently causal mutations in four genes known to cause Mendelian disease (TCF4, EFTUD2, SCN2A and SMAD4) and one gene related to known Mendelian disease genes (NGLY1). Of particular interest is that at the time of this study, EFTUD2 was not yet known as a Mendelian disease gene but was nominated as a likely cause based on the observation of de novo mutations in two unrelated probands. In a seventh case with multiple disparate clinical features, the authors were able to identify homozygous mutations in EFEMP1 as a likely cause for macular degeneration (though likely not for other features).
This study provides evidence that next-generation sequencing can have high success rates in a clinical setting, but also highlights key challenges. It further suggests that the presentation of known Mendelian conditions may be considerably broader than currently recognised.
Journal of Medical Genetics 05/2012; 49(6):353-61. · 6.36 Impact Factor
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Heather C Mefford,
Jill A Rosenfeld,
Natasha Shur,
Anne M Slavotinek,
Victoria A Cox,
Raoul C Hennekam,
Helen V Firth,
Lionel Willatt,
Patricia Wheeler,
Eric M Morrow, [......],
Susan Zelewski,
Valerie Banks,
Wendy Smith,
Rosemarie Smith,
Lindsay Paull,
Kenneth N Rosenbaum,
David J Amor,
Joao Silva,
Allen Lamb,
Evan E Eichler
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ABSTRACT: Chromosome 15q24 microdeletion syndrome is a rare genomic disorder characterised by intellectual disability, growth retardation, unusual facial morphology and other anomalies. To date, 20 patients have been reported; 18 have had detailed breakpoint analysis.
To further delineate the features of the 15q24 microdeletion syndrome, the clinical and molecular characterisation of fifteen patients with deletions in the 15q24 region was performed, nearly doubling the number of reported patients.
Breakpoints were characterised using a custom, high-density array comparative hybridisation platform, and detailed phenotype information was collected for each patient.
Nine distinct deletions with different breakpoints ranging in size from 266 kb to 3.75 Mb were identified. The majority of breakpoints lie within segmental duplication (SD) blocks. Low sequence identity and large intervals of unique sequence between SD blocks likely contribute to the rarity of 15q24 deletions, which occur 8-10 times less frequently than 1q21 or 15q13 microdeletions in our series. Two small, atypical deletions were identified within the region that help delineate the critical region for the core phenotype in the 15q24 microdeletion syndrome.
The molecular characterisation of these patients suggests that the core cognitive features of the 15q24 microdeletion syndrome, including developmental delays and severe speech problems, are largely due to deletion of genes in a 1.1-Mb critical region. However, genes just distal to the critical region also play an important role in cognition and in the development of characteristic facial features associated with 15q24 deletions. Clearly, deletions in the 15q24 region are variable in size and extent. Knowledge of the breakpoints and size of deletion combined with the natural history and medical problems of our patients provide insights that will inform management guidelines. Based on common phenotypic features, all patients with 15q24 microdeletions should receive a thorough neurodevelopmental evaluation, physical, occupational and speech therapies, and regular audiologic and ophthalmologic screening.
Journal of Medical Genetics 12/2011; 49(2):110-8. · 6.36 Impact Factor
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Timothy W Yu,
Ganeshwaran H Mochida,
David J Tischfield,
Sema K Sgaier,
Laura Flores-Sarnat,
Consolato M Sergi,
Meral Topçu, Marie T McDonald,
Brenda J Barry,
Jillian M Felie,
Christine Sunu,
William B Dobyns,
Rebecca D Folkerth,
A James Barkovich,
Christopher A Walsh
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ABSTRACT: Genes associated with human microcephaly, a condition characterized by a small brain, include critical regulators of proliferation, cell fate and DNA repair. We describe a syndrome of congenital microcephaly and diverse defects in cerebral cortical architecture. Genome-wide linkage analysis in two families identified a 7.5-Mb locus on chromosome 19q13.12 containing 148 genes. Targeted high throughput sequence analysis of linked genes in each family yielded > 4,000 DNA variants and implicated a single gene, WDR62, as harboring potentially deleterious changes. We subsequently identified additional WDR62 mutations in four other families. Magnetic resonance imaging and postmortem brain analysis supports important roles for WDR62 in the proliferation and migration of neuronal precursors. WDR62 is a WD40 repeat-containing protein expressed in neuronal precursors as well as in postmitotic neurons in the developing brain and localizes to the spindle poles of dividing cells. The diverse phenotypes of WDR62 suggest it has central roles in many aspects of cerebral cortical development.
Nature Genetics 10/2010; 42(11):1015-20. · 35.53 Impact Factor
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Santhosh Girirajan,
Jill A Rosenfeld,
Gregory M Cooper,
Francesca Antonacci,
Priscillia Siswara,
Andy Itsara,
Laura Vives,
Tom Walsh,
Shane E McCarthy,
Carl Baker, [......],
Eric Haan,
Kathryn L Friend,
Marco Fichera,
Corrado Romano,
Jozef Gécz,
Lynn E DeLisi,
Jonathan Sebat,
Mary-Claire King,
Lisa G Shaffer,
Evan E Eichler
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ABSTRACT: We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls (P = 0.0009, OR = 7.2) and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls (P = 0.028, OR = 2.5). Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents (P = 0.037, OR = 6). Probands were more likely to carry an additional large copy-number variant when compared to matched controls (10 of 42 cases, P = 5.7 x 10(-5), OR = 6.6). The clinical features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease.
Nature Genetics 02/2010; 42(3):203-9. · 35.53 Impact Factor
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ABSTRACT: A total of 124 individuals were tested in the initial 9 months that array CGH technology was offered to clinical genetics patients. In 11 of these patients array CGH identified a previously unsuspected diagnosis. A suspected diagnosis was confirmed in three patients. A single case in this series proved to be a polymorphic copy number variant. This paper describes five of the patients with previously unsuspected diagnoses in detail. We suggest that array CGH is an improved tool ready for routine use in clinical genetics.
American Journal of Medical Genetics Part A 11/2006; 140(19):2050-6. · 2.39 Impact Factor
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ABSTRACT: We report the case of a male infant with incontinentia pigmenti (MIM 308310) and low-grade XXY mosaicism. Fluorescence in situ hybridization may reveal the underlying genetic alteration in male patients with incontinentia pigmenti and a normal karyotype.
Journal of the American Academy of Dermatology 08/2006; 55(1):136-8. · 3.99 Impact Factor
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ABSTRACT: Congenital Pelger-Huët anomaly (PHA) is an autosomal dominant disorder characterized by hypolobulated neutrophils with coarse clumping of the nuclear chromatin. PHA has been recently linked to the gene encoding the lamin B receptor, located at chromosome 1q41-43. The authors report a case of PHA in a child with interstitial deletion of the 1q subtelomeric region (1q42.3-44), providing supportive evidence to this linkage. All neutrophils in the peripheral blood smear had the characteristic unsegmented or bilobed appearance. Additional features in this child included failure to thrive, developmental delay, cleft palate, seizure disorder, and dysmorphic facial features.
Pediatric Blood & Cancer 06/2006; 46(5):645-8. · 1.89 Impact Factor
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ABSTRACT: We report on an infant referred for chromosome analysis during the neonatal period due to ambiguous genitalia. The genitalia appeared male with bilaterally palpable testes, penoscrotal hypospadias, chordee, and a bifid scrotum. Chromosome analysis and interphase FISH analysis of lymphocytes showed a 45,X karyotype and no evidence for SRY in 200 nuclei examined, respectively. Subsequent chromosome analysis of fibroblasts revealed a 69,XXY karyotype. Molecular studies were carried out to determine the etiology of the chromosome findings. Results indicated that the two cell lines are mosaic rather than chimeric and that the triploidy resulted from delayed dispermy rather than delayed polar body inclusion. To our knowledge this is the first reported living individual with (near) diploid/triploid mosaicism for 45,X/69,XXY.
American Journal of Medical Genetics Part A 11/2005; 138A(2):171-4. · 2.39 Impact Factor
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Jennifer J Johnston,
Isabelle Olivos-Glander,
Christina Killoran,
Emma Elson,
Joyce T Turner,
Kathryn F Peters,
Margaret H Abbott,
David J Aughton,
Arthur S Aylsworth,
Michael J Bamshad, [......],
John A Phillips,
Laurie S Sadler,
Joan M Stoler,
David Tilstra,
Catherine M Walsh Vockley,
Elaine H Zackai,
Touran M Zadeh,
Louise Brueton,
Graeme Charles M Black,
Leslie G Biesecker
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ABSTRACT: Mutations in the GLI3 zinc-finger transcription factor gene cause Greig cephalopolysyndactyly syndrome (GCPS) and Pallister-Hall syndrome (PHS), which are variable but distinct clinical entities. We hypothesized that GLI3 mutations that predict a truncated functional repressor protein cause PHS and that functional haploinsufficiency of GLI3 causes GCPS. To test these hypotheses, we screened patients with PHS and GCPS for GLI3 mutations. The patient group consisted of 135 individuals: 89 patients with GCPS and 46 patients with PHS. We detected 47 pathological mutations (among 60 probands); when these were combined with previously published mutations, two genotype-phenotype correlations were evident. First, GCPS was caused by many types of alterations, including translocations, large deletions, exonic deletions and duplications, small in-frame deletions, and missense, frameshift/nonsense, and splicing mutations. In contrast, PHS was caused only by frameshift/nonsense and splicing mutations. Second, among the frameshift/nonsense mutations, there was a clear genotype-phenotype correlation. Mutations in the first third of the gene (from open reading frame [ORF] nucleotides [nt] 1-1997) caused GCPS, and mutations in the second third of the gene (from ORF nt 1998-3481) caused primarily PHS. Surprisingly, there were 12 mutations in patients with GCPS in the 3' third of the gene (after ORF nt 3481), and no patients with PHS had mutations in this region. These results demonstrate a robust correlation of genotype and phenotype for GLI3 mutations and strongly support the hypothesis that these two allelic disorders have distinct modes of pathogenesis.
The American Journal of Human Genetics 05/2005; 76(4):609-22. · 10.60 Impact Factor
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Regina E Ensenauer,
Adewale Adeyinka,
Heather C Flynn,
Virginia V Michels,
Noralane M Lindor,
D Brian Dawson,
Erik C Thorland,
Cindy Pham Lorentz,
Jennifer L Goldstein, Marie T McDonald,
Wendy E Smith,
Elba Simon-Fayard,
Alan A Alexander,
Anita S Kulharya,
Rhett P Ketterling,
Robin D Clark,
Syed M Jalal
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ABSTRACT: Chromosome 22, particularly band 22q11.2, is predisposed to rearrangements due to misalignments of low-copy repeats (LCRs). DiGeorge/velocardiofacial syndrome (DG/VCFS) is a common disorder resulting from microdeletion within the same band. Although both deletion and duplication are expected to occur in equal proportions as reciprocal events caused by LCR-mediated rearrangements, very few microduplications have been identified. We have identified 13 cases of microduplication 22q11.2, primarily by interphase fluorescence in situ hybridization (FISH). The size of the duplications, determined by FISH probes from bacterial artificial chromosomes and P(1) artificial chromosomes, range from 3-4 Mb to 6 Mb, and the exchange points seem to involve an LCR. Molecular analysis based on 15 short tandem repeats confirmed the size of the duplications and indicated that at least 1 of 15 loci has three alleles present. The patients' phenotypes ranged from mild to severe, sharing a tendency for velopharyngeal insufficiency with DG/VCFS but having other distinctive characteristics, as well. Although the present series of patients was ascertained because of some overlapping features with DG/VCF syndromes, the microduplication of 22q11.2 appears to be a new syndrome.
The American Journal of Human Genetics 12/2003; 73(5):1027-40. · 10.60 Impact Factor
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Dwight D Koeberl,
Sarah P Young,
Niels S Gregersen,
Jerry Vockley,
Wendy E Smith,
Daniel Kelly Benjamin,
Yan An,
Susan D Weavil,
Shu H Chaing,
Deeksha Bali, Marie T McDonald,
Priya S Kishnani,
Y-T Chen,
David S Millington
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ABSTRACT: Tandem mass spectrometry was adopted for newborn screening by North Carolina in April 1999. Since then, three infants with short-chain acyl-CoA dehydrogenase (SCAD) and one with isobutyryl-CoA dehydrogenase deficiency were detected on the basis of elevated butyrylcarnitine/isobutyrylcarnitine (C4-carnitine) concentrations in newborn blood spots analyzed by tandem mass spectrometry. For three SCAD-deficient infants, biochemical evaluation included a plasma acylcarnitine profile with markedly elevated C4-carnitine, urine organic acid analysis with markedly elevated ethylmalonic and 2-methylsuccinic acids, and markedly elevated [U-13C]butyrylcarnitine concentrations in medium from fibroblasts incubated with [U-13C]palmitic acid and excess l-carnitine, consistent with classic SCAD deficiency. Two of three infants diagnosed with classic SCAD deficiency remained asymptomatic; however, the third infant presented with seizures and a cerebral infarct at 10 wk of age. All three infants had putatively inactivating mutations in both alleles of the SCAD gene. The highly elevated plasma C4-carnitine levels in the three infants detected by newborn screening tandem mass spectrometry differentiated them from infants and children who were homozygous or compound heterozygous for one of two SCAD gene susceptibility variations; for the latter group the C4-carnitine levels were normal. Isobutyryl-CoA dehydrogenase deficiency in a fourth infant was confirmed after isolated elevation of C4-carnitine in the acylcarnitine profile.
Pediatric Research 09/2003; 54(2):219-23. · 2.70 Impact Factor
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ABSTRACT: We describe a case of XY sex reversal, gonadal dysgenesis, and gonadoblastoma in a patient with a deletion of 9p24 due to a familial translocation. The rearranged chromosome 9 was inherited from the father; the patient's karyotype was 46,XY,der(9)t(8;9)(p21;p24)pat. A review shows that 6 additional patients with 46,XY sex reversal associated with monosomy of the distal short arm of chromosome 9 have been observed. The observation that all 7 patients with sex reversal share a deletion of the distal short arm of chromosme 9 is consistent with the hypothesis that the region 9p24 contains a gene or genes necessary for male sex determination. This present case narrows the chromosome interval containing a critical sex determination gene to the relatively small region 9p24. A molecular analysis of this region will provide a means to identify a gene invoved in male sex determination. Am. J. Med. Genet. 73:321–326, 1997. © 1997 Wiley-Liss, Inc. Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/38270/1/17_ftp.pdf
