L G Shaffer

McGill University, Montréal, Quebec, Canada

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Publications (136)676 Total impact

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    ABSTRACT: Microduplications of the Sotos syndrome region containing NSD1 on 5q35 have recently been proposed to cause a syndrome of microcephaly, short stature and developmental delay. To further characterize this emerging syndrome, we report the clinical details of 12 individuals from 8 families found to have interstitial duplications involving NSD1, ranging in size from 370 kb to 3.7 Mb. All individuals are microcephalic, and height and childhood weight range from below average to severely restricted. Mild-to-moderate learning disabilities and/or developmental delay are present in all individuals, including carrier family members of probands; dysmorphic features and digital anomalies are present in a majority. Craniosynostosis is present in the individual with the largest duplication, though the duplication does not include MSX2, mutations of which can cause craniosynostosis, on 5q35.2. A comparison of the smallest duplication in our cohort that includes the entire NSD1 gene to the individual with the largest duplication that only partially overlaps NSD1 suggests that whole-gene duplication of NSD1 in and of itself may be sufficient to cause the abnormal growth parameters seen in these patients. NSD1 duplications may therefore be added to a growing list of copy number variations for which deletion and duplication of specific genes have contrasting effects on body development.
    Molecular syndromology 01/2013; 3(6):247-254.
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    ABSTRACT: TBR1 encodes a transcription factor with critical roles in corticogenesis, including cortical neuron migration and axon pathfinding, establishment of regional and laminar identity of cortical neurons, and control of glutamatergic neuronal cell fate. Based upon TBR1's role in cortical development, we sought to investigate TBR1 hemizygosity in individuals referred for genetic evaluation of intellectual disability and developmental delay. We describe 4 patients with microdeletions identified by molecular cytogenetic techniques, encompassing TBR1 and spanning 2q24.1q31.1, ranging in size from 2.17 to 12.34 Mb. Only the patient with the largest deletion had a possible cortical malformation. Mild ventriculomegaly is the only common brain anomaly, present in all patients; a Chiari I malformation is seen in 2 patients, and mega cisterna magna is seen in a third. Our findings are consistent with Tbr1 mouse models showing that hemizygosity of the gene requires additional genetic factors for the manifestation of severe structural brain malformations. Other syndromic features are present in these patients, including autism spectrum disorders, ocular colobomas, and craniosynostosis, features that are likely affected by the deletion of genes other than TBR1.
    Molecular syndromology 09/2012; 3(3):102-112.
  • Molecular syndromology 01/2012; 3:247-254.
  • Leukemia: official journal of the Leukemia Society of America, Leukemia Research Fund, U.K 03/2011; 25(6):1042-6. · 10.16 Impact Factor
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    ABSTRACT: Background: Deletions that encompass 2q31.1 have been proposed as a microdeletion syndrome with common clinical features, including intellectual disability/developmental delay, microcephaly, cleft palate, growth delay, and hand/foot anomalies. In addition, several genes within this region have been proposed as candidates for split hand-foot malformation 5 (SHFM5). Methods: To delineate the genotype-phenotype correlation between deletions of this region, we identified 14 individuals with deletions at 2q31.1 detected by microarray analysis for physical and developmental disabilities. Results: All subjects for whom detailed clinical records were available had neurological deficits of varying degree. Seven subjects with deletions encompassing the HOXD cluster had hand/foot anomalies of varying severity, including syndactyly, brachydactyly, and ectrodactyly. Of 7 subjects with deletions proximal to the HOXD cluster, 5 of which encompassed DLX1/DLX2, none had clinically significant hand/foot anomalies. In contrast to previous reports, the individuals in our study did not display a characteristic gestalt of dysmorphic facial features. Conclusion: The absence of hand/foot anomalies in any of the individuals with deletions of DLX1/DLX2 but not the HOXD cluster supports the hypothesis that haploinsufficiency of the HOXD cluster, rather than DLX1/DLX2, accounts for the skeletal abnormalities in subjects with 2q31.1 microdeletions.
    Molecular syndromology 01/2010; 1(5):262-271.
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    ABSTRACT: We report the identification of microdeletions of 16q11.2q12.2 by microarray-based comparative genomic hybridization (aCGH) in two individuals. The clinical features of these two individuals include hypotonia, gastroesophageal reflux, ear anomalies, and toe deformities. Other features include developmental delay, mental retardation, hypothyroidism, and seizures. The identification of common clinical features in these two individuals and those of one other report suggests microdeletion of 16q12.1q12.2 is a rare, emerging syndrome. These results illustrate that aCGH is particularly suited to identify rare chromosome abnormalities in patients with apparently non-syndromic idiopathic mental retardation and birth defects.
    Clinical Genetics 10/2008; 74(5):469-75. · 4.25 Impact Factor
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    ABSTRACT: Array-based comparative genomic hybridization (array CGH) is an emerging technology that allows for the genome-wide detection of DNA copy number changes (CNC) such as deletions or duplications. In this study, array-based CGH was applied to a consecutive series of children with previously undiagnosed non-syndromal global developmental delay (GDD) to assess potential etiologic yield. The children in this study were drawn from a previously reported consecutive series of children with well-defined GDD. Almost all subjects had undergone prior karyotyping and neuroimaging studies with non-diagnostic results. Array-based CGH was undertaken using the SignatureChip(R) (1887 BACs representing 622 loci) with abnormalities verified by subsequent FISH analysis and testing of parents to distinguish between pathogenic and familial non-pathogenic variants. On CGH analysis in our study, 6 of 94 children (6.4%) had a causally related pathogenic CNC. Three were sub-telomeric in location. An analysis of a variety of clinical factors revealed that only the presence of minor dysmorphic features (<3) was predictive of etiologic yield on CGH analysis (4/26 vs. 2/68, P = 0.05). Severity of delay was not found to be predictive. In children with non-syndromal GDD, array-based CGH has an etiologic yield of 6.4%. This suggests that this emerging technology may be of diagnostic value when applied subsequent to detailed history, physical examination, and targeted laboratory testing. Array CGH may merit consideration as a first-tier test in the context of a child with unexplained GDD.
    American Journal of Medical Genetics Part B Neuropsychiatric Genetics 04/2008; 147B(7):1101-8. · 3.23 Impact Factor
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    ABSTRACT: Comprehensive and reliable testing is an important component of counseling and management in clinical genetics. Identification of imbalances of chromosomal segments has uncovered new genes and has established phenotype/genotype correlations for many syndromes with previously unidentified causes. Conventional cytogenetics has proven to be useful for the detection of large aberrations, but its resolution limits the identification of submicroscopic alterations. Comparative genomic hybridization (CGH) on a microarray-based platform has the potential to detect and characterize both microscopic and submicroscopic chromosomal abnormalities. Nine cases of aberrations involving chromosome 18 are used to illustrate the use and clinical potential of array CGH.
    Cytogenetic and Genome Research 02/2006; 114(3-4):379-83. · 1.84 Impact Factor
  • L G Shaffer, B A Bejjani
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    ABSTRACT: Microarray-based comparative genomic hybridization (array CGH) merges molecular diagnostics with traditional chromosome analysis and is transforming the field of cytogenetics. Prospective studies of individuals with developmental delay and dysmorphic features have demonstrated that array CGH has the ability to detect any genomic imbalance including deletions, duplications, aneuploidies and amplifications. Detection rates for chromosome abnormalities with array CGH range from 5-17% in individuals with normal results from prior routine cytogenetic testing. In addition, copy number variants (CNVs) were identified in all studies. These CNVs may include large-scale variation and can confound the diagnostic interpretations. Although cytogeneticists will require additional training and laboratories must become appropriately equipped, array CGH holds the promise of being the initial diagnostic tool in the identification of visible and submicroscopic chromosome abnormalities in mental retardation and other developmental disabilities.
    Cytogenetic and Genome Research 02/2006; 115(3-4):303-9. · 1.84 Impact Factor
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    ABSTRACT: We report a case of a patient with omphalocele, dysmorphic features, and mild developmental delay associated with a chromosomal aberration. Chromosome studies showed that the propositus carries a maternally derived unbalanced translocation der(4)t(3;4)(q27.3;q32.3), resulting in trisomy for region 3q27.3-->qter and monosomy for 4q32.3-->qter. Because the association between dup3q and omphalocele has been reported in several cases, we analyzed the data on 93 previously reported patients with partial trisomy of the long arm of chromosome 3 and compared the clinical features between the cases. The imbalance of chromosome 3 in the patient was further defined by fluorescence in situ hybridization (FISH) studies using bacterial artificial chromosome (BAC) clones. BAC clone RP11-171N2 was identified as a breakpoint-spanning clone in the patient and his mother. Based on our comparative analysis, we have delineated that the smallest region of overlap (SRO) associated with omphalocele is from BAC 171N2 to 3qter. We hypothesize that the SRO contains a gene(s) important in normal abdominal wall development and is of potential interest for further investigation.
    Clinical Genetics 11/2003; 64(5):404-13. · 3.94 Impact Factor
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    ABSTRACT: Monosomy 1p36 is a relatively common chromosome deletion. Deletion of this chromosome band can be difficult to visualize using routine cytogenetic banding techniques. The use of fluorescence in situ hybridization (FISH) with telomere region-specific probes has aided in the diagnosis of patients. In this study we ascertained 62 patients with deletions of 1p36 from 61 families and collected information regarding previous chromosome analyses, mode of ascertainment, clinical indication, age at diagnosis, and parental ages. The majority of deletions occur on the maternally derived chromosome. We identified terminal deletions, interstitial deletions, derivative chromosomes, and complex rearrangements. We correlated the type of rearrangement with the parental origins. Almost 50% of the patients had at least one chromosome analysis interpreted as normal. Retrospectively, 98% of deletions could be identified by routine chromosome analysis with careful attention to chromosome 1p36. Clinical indications were variable, with developmental delay/mental retardation being the most common. Increased maternal serum alpha fetoprotein (MSAFP) was detected in four of the five prenatally diagnosed cases. Maternal age at the time of birth of the affected child was significantly lower than the general United States population mean. We suggest a multistep approach for the diagnosis and clinical evaluation in cases of monosomy 1p36.
    Clinical Genetics 11/2003; 64(4):310-6. · 3.94 Impact Factor
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    ABSTRACT: Heilstedt HA, Ballif BC, Howard LA, Kashork CD and Shaffer LG. Population data suggest that deletions of 1p36 are a relatively common chromosome abnormality. Monosomy 1p36 is a relatively common chromosome deletion. Deletion of this chromosome band can be difficult to visualize using routine cytogenetic banding techniques. The use of fluorescence in situ hybridization (FISH) with telomere region-specific probes has aided in the diagnosis of patients. In this study we ascertained 62 patients with deletions of 1p36 from 61 families and collected information regarding previous chromosome analyses, mode of ascertainment, clinical indication, age at diagnosis, and parental ages. The majority of deletions occur on the maternally derived chromosome. We identified terminal deletions, interstitial deletions, derivative chromosomes, and complex rearrangements. We correlated the type of rearrangement with the parental origins. Almost 50% of the patients had at least one chromosome analysis interpreted as normal. Retrospectively, 98% of deletions could be identified by routine chromosome analysis with careful attention to chromosome 1p36. Clinical indications were variable, with developmental delay/mental retardation being the most common. Increased maternal serum alpha fetoprotein (MSAFP) was detected in four of the five prenatally diagnosed cases. Maternal age at the time of birth of the affected child was significantly lower than the general United States population mean. We suggest a multistep approach for the diagnosis and clinical evaluation in cases of monosomy 1p36.
    Clinical Genetics 10/2003; 64(4):310-316. · 3.94 Impact Factor
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    ABSTRACT: The recent demonstration of genomic imprinting of DLK1 and MEG3 on human chromosome 14q32 indicates that these genes might contribute to the discordant phenotypes associated with uniparental disomy (UPD) of chromosome 14. Regulation of imprinted expression of DLK1 and MEG3 involves a differentially methylated region (DMR) that encompasses the MEG3 promoter. We exploited the normal differential methylation of the DLK1/MEG3 region to develop a rapid diagnostic PCR assay based upon an individual's epigenetic profile. We used methylation-specific multiplex PCR in a retrospective analysis to amplify divergent lengths of the methylated and unmethylated MEG3 DMR in a single reaction and accurately identified normal, maternal UPD14, and paternal UPD14 in bisulfite converted DNA samples. This approach, which is based solely on differential epigenetic profiles, may be generally applicable for rapidly and economically screening for other imprinting defects associated with uniparental disomy, determining loss of heterozygosity of imprinted tumor suppressor genes, and identifying gene-specific hypermethylation events associated with neoplastic progression.
    Human Mutation 08/2003; 22(1):92-7. · 5.21 Impact Factor
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    ABSTRACT: Obsessive-compulsive disorder (OCD) is a chronic psychiatric disease characterized by recurrent obsessions, compulsions, or both. The prevalence rate of OCD is 2.1% in the general population. Here we report cytogenetic analysis of 26 patients affected with OCD. In one male patient (OCD-K33), we identified a fragile X chromosome by cytogenetic analysis with 21% of cells demonstrating a fragile site at Xq27-q28. Polymerase chain reaction (PCR) and Southern blot analysis demonstrated that the molecular basis of the OCD-K33 fragile X chromosome was expansion of the CCG repeat at FRAXE. The number of the expanded repeats was estimated to be more than 300 copies, qualifying it as a full FRAXE mutation. Further analysis of the family members of OCD-K33 revealed another member with a full FRAXE mutation (630-1,200 copies of the CCG repeat), who had the clinical phenotype of speech impairment, and two other members with normal phenotypes and no FRAXE expansion. The two FRAXE expansions lead to complete methylation at the CCG repeat. The co-segregation of the full FRAXE mutation with apparent neurologic disorders in the same family provides further support to the notion that FRAXE is a genetic neurologic condition. Our findings expand the spectrum of clinical phenotypes associated with FRAXE mutations.
    American Journal of Medical Genetics Part A 05/2003; 118A(1):25-8. · 2.30 Impact Factor
  • LISA G  SHAFFER 
    Fetal and Maternal Medicine Review 04/2003; 14(02):155 - 175.
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    Journal of Medical Genetics 04/2003; 40(3):e26. · 5.70 Impact Factor
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    ABSTRACT: We report a 5-year-old boy with a small de novo marker chromosome derived from the proximal short arm of chromosome 17. His clinical features include hypotonia, global developmental delay, oval face with large nose and prominent ears, and ligamentous laxity of the fingers. Magnetic resonance imaging of the brain demonstrated mildly delayed myelination. G-band chromosome analysis revealed mosaicism for a small marker chromosome in 85% of the peripheral blood cells analyzed. Fluorescence in situ hybridization and microsatellite polymorphism studies showed that the der(17) was of maternal origin and included genetic material from the 17p10-p12 region, but did not contain the PMP22 gene. One breakpoint mapped within the centromere and the second breakpoint mapped adjacent to the Charcot–Marie–Tooth disease type 1A proximal low-copy repeat (CMT1A-REP). We compare the clinical characteristics of our patient with those previously reported to have a duplication involving the proximal short arm region of chromosome 17 to further delineate the phenotype of trisomy 17p10-p12.
    Clinical Genetics 11/2002; 60(5):336-344. · 3.94 Impact Factor
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    ABSTRACT: Poly(ADP-ribose) polymerase 2 (PARP-2) is a newly discovered member of the PARP family. We report the association of PARP-2 with mammalian centromeres in a cell-cycle-dependent manner, accumulating at centromeres during prometaphase and metaphase, disassociating during anaphase, and disappearing from the centromeres by telophase. Analysis of a pseudodicentric chromosome and a human neocentromere indicates that PARP-2 binding occurs only at active centromeres in a sequence-independent manner. Centromere binding peaks at the outer centromere region, and is significantly enhanced upon treatment with microtubule-inhibiting drugs. Co-immunoprecipitation assay demonstrates interaction between PARP-2 and its functional homolog PARP-1, constitutive centromere proteins Cenpa and Cenpb, and spindle checkpoint protein Bub3, but not with a third constitutive centromere protein Cenpc. These results, together with our previous demonstration that PARP-1 displays an identical binding pattern with Cenpa, Cenpb and Bub3, but not Cenpc, and that all three proteins undergo significant poly(ADP-ribosyl)ation upon gamma-irradiation of cells, point to possible diverse roles of PARP-2 and PARP-1 in modulating the structure and checkpoint functions of the mammalian centromere, in particular during radiation-induced DNA damage.
    Human Molecular Genetics 10/2002; 11(19):2319-29. · 7.69 Impact Factor
  • Sung-Ryul Kim, Lisa G Shaffer
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    ABSTRACT: Robertsonian translocations (ROBs) are rearrangements of the acrocentric chromosomes 13-15 and 21-22. Cytologically, ROBs between homologous chromosomes cannot be distinguished from isochromosomes that originate through duplication of a single homologue. Both types of rearrangements can be involved in aneuploidy. A conceptus with a trisomy or a monosomy can be rescued, and in a proportion of cases, a uniparental disomy (UPD) would result. If there are regions of genome imprinting on a uniparental chromosome pair, phenotypic consequences can result. Chromosomes 14 and 15 are imprinted, and UPD of these are known to result in abnormalities. Thus, prenatal testing should be considered in all pregnancies when one of the parents is a balanced carrier of a ROB because of the risk for aneuploidy, and UPD testing should be considered in fetuses found to carry a balanced ROB or isochromosome that involves chromosomes 14 or 15. Additionally, infants or children with congenital anomalies who carry a ROB should also be considered for UPD testing.
    Genetic Testing 02/2002; 6(3):163-8. · 1.17 Impact Factor
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    ABSTRACT: Incontinentia pigmenti (IP), or "Bloch-Sulzberger syndrome," is an X-linked dominant disorder characterized by abnormalities of skin, teeth, hair, and eyes; skewed X-inactivation; and recurrent miscarriages of male fetuses. IP results from mutations in the gene for NF-kappaB essential modulator (NEMO), with deletion of exons 4-10 of NEMO accounting for >80% of new mutations. Male fetuses inheriting this mutation and other "null" mutations of NEMO usually die in utero. Less deleterious mutations can result in survival of males subjects, but with ectodermal dysplasia and immunodeficiency. Male patients with skin, dental, and ocular abnormalities typical of those seen in female patients with IP (without immunodeficiency) are rare. We investigated four male patients with clinical hallmarks of IP. All four were found to carry the deletion normally associated with male lethality in utero. Survival in one patient is explained by a 47,XXY karyotype and skewed X inactivation. Three other patients possess a normal 46,XY karyotype. We demonstrate that these patients have both wild-type and deleted copies of the NEMO gene and are therefore mosaic for the common mutation. Therefore, the repeat-mediated rearrangement leading to the common deletion does not require meiotic division. Hypomorphic alleles, a 47,XXY karyotype, and somatic mosaicism therefore represent three mechanisms for survival of males carrying a NEMO mutation.
    The American Journal of Human Genetics 01/2002; 69(6):1210-7. · 11.20 Impact Factor

Publication Stats

4k Citations
676.00 Total Impact Points

Institutions

  • 2008
    • McGill University
      • Department of Pediatrics
      Montréal, Quebec, Canada
  • 2003
    • Lerner Research Institute
      Cleveland, Ohio, United States
    • Washington State University
      • School of Molecular Biosciences
      Pullman, WA, United States
  • 1993–2003
    • Baylor College of Medicine
      • Department of Molecular & Human Genetics
      Houston, TX, United States
  • 2002
    • Ulsan University Hospital
      Urusan, Ulsan, South Korea
  • 2001
    • University of California, Davis
      • Department of Obstetrics and Gynecology
      Davis, CA, United States
  • 1992–2000
    • The Royal Children's Hospital
      Melbourne, Victoria, Australia
  • 1998
    • University of Alabama at Birmingham
      • Department of Neurology
      Birmingham, AL, United States
  • 1997
    • University of Texas Medical School
      Houston, Texas, United States
    • Albert Einstein Medical Center
      Philadelphia, Pennsylvania, United States
  • 1995
    • Advocate Lutheran General Hospital
      Chicago, Illinois, United States
    • Australian National University
      • Molecular Bioscience Department
      Canberra, Australian Capital Territory, Australia
  • 1994
    • Dong-A University
      Tsau-liang-hai, Busan, South Korea