Hancks D.C.,University of Pennsylvania |
Hancks D.C.,McKusick Nathans Institute for Genetic Medicine |
Goodier J.L.,McKusick Nathans Institute for Genetic Medicine |
Mandal P.K.,McKusick Nathans Institute for Genetic Medicine |
And 2 more authors.
Human Molecular Genetics | Year: 2011
Human retrotransposons generate structural variation and genomic diversity through ongoing retrotransposition and non-allelic homologous recombination. Cell culture retrotransposition assays have provided great insight into the genomic impact of retrotransposons, in particular, LINE-1(L1) and Alu elements; however, no such assay exists for the youngest active human retrotransposon, SINE-VNTR-Alu (SVA). Here we report the development of an SVA cell culture retrotransposition assay. We marked several SVAs with either neomycin or EGFP retrotransposition indicator cassettes. Engineered SVAs retrotranspose using L1 proteins supplemented in trans in multiple cell lines, including U2OS osteosarcoma cells where SVA retrotransposition is equal to that of an engineered L1. Engineered SVAs retrotranspose at 1-54 times the frequency of a marked pseudogene in HeLa HA cells. Furthermore, our data suggest a variable requirement for L1 ORF1p for SVA retrotransposition. Recovered engineered SVA insertions display all the hallmarks of LINE-1 retrotransposition and some contain 5′ and 3′ transductions, which are common for genomic SVAs. Of particular interest is the fact that four out of five insertions recovered from one SVA are full-length, with the 5′ end of these insertions beginning within 5 nt of the CMV promoter transcriptional start site. This assay demonstrates that SVA elements are indeed mobilized in trans by L1. Previously intractable questions regarding SVA biology can now be addressed. © The Author 2011. Published by Oxford University Press. All rights reserved.
PubMed | Brigham and Women's Hospital, Johns Hopkins University, Yale University, McKusick Nathans Institute for Genetic Medicine and Virginia Polytechnic Institute and State University
Type: | Journal: Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation | Year: 2016
Numerous factors associate with health disparities. The extent to which such factors influence health-related quality of life (HRQOL) among adults with short stature skeletal dysplasias (SD) is unknown. In an effort to update and clarify knowledge about the HRQOL of adults with SD, this study aimed to quantify HRQOL scores relative to the American average and assess whether specific indicators are associated with lower scores.Members (>18years) of Little People of America were invited to complete an online survey assessing HRQOL using the SF-12 supplemented with indicator-specific questions. SF-12 components (Physical Component Summary, PCS; Mental Component Summary, MCS) were compared to the standardized national American mean. Scores were divided at the median to identify factors associated with lower scores using multivariable logistic regression, adjusting for age, gender, race, education, and employment.A total of 189 surveys were completed. Mean and median PCS and MCS were below the national mean of 50 (p<0.001). Advancing decade of age corresponded to a significant decline in PCS (p<0.001) but not MCS (p=0.366). Pain prevalence was high (79.4%); however, only 5.9% visited a pain specialist. Significant factors for lower PCS included age >40years (p=0.020), having spondyloepiphyseal dysplasia congenita (SED) or diastrophic dysplasia relative to achondroplasia (p=0.023), pain (p<0.001), and partial versus full health insurance coverage (p=0.034). For MCS, significant factors included a lack of social support (p=0.002) and being treated differently/feeling stigmatized by health care providers (p=0.022).Individuals with SD face documented disparities and report lower HRQOL. Further research and interventions are needed to modify nuanced factors influencing these results and address the high prevalence of pain.
Baetens M.,Ghent University |
Van Laer L.,University of Antwerp |
De Leeneer K.,Ghent University |
Hellemans J.,Ghent University |
And 11 more authors.
Human Mutation | Year: 2011
The Marfan (MFS) and Loeys-Dietz (LDS) syndromes are caused by mutations in the fibrillin-1 (FBN1) and Transforming Growth Factor Beta Receptor 1 and 2 (TGFBR1 and TGFBR2) genes, respectively. With the current conventional mutation screening technologies, analysis of this set of genes is time consuming and expensive. We have tailored a cost-effective and reliable mutation discovery strategy using multiplex PCR followed by Next Generation Sequencing (NGS). In a first stage, genomic DNA from five MFS or LDS patient samples with previously identified mutations and/or polymorphisms in FBN1 and TGFBR1 and 2 were analyzed and revealed all expected variants. In a second stage, we validated the technique on 87 samples from MFS patients fulfilling the Ghent criteria. This resulted in the identification of 75 FBN1 mutations, of which 67 were unique. Subsequent Multiplex Ligation-dependent Probe Amplification (MLPA) analysis of the remaining negative samples identified four large deletions/insertions. Finally, Sanger sequencing identified a missense mutation in FBN1 exon 1 that was not included in the NGS workflow. In total, there was an overall mutation identification rate of 92%, which is in agreement with data published previously. We conclude that multiplex PCR of all coding exons of FBN1 and TGFBR1/2 followed by NGS analysis and MLPA is a robust strategy for time- and cost-effective identification of mutations. © 2011 Wiley-Liss, Inc.
Feyder M.,McKusick Nathans Institute for Genetic Medicine |
Goff L.A.,McKusick Nathans Institute for Genetic Medicine |
Goff L.A.,Johns Hopkins University
Journal of Clinical Investigation | Year: 2016
The number of long noncoding RNAs (lncRNAs) has grown rapidly; however, our understanding of their function remains limited. Although cultured cells have facilitated investigations of lncRNA function at the molecular level, the use of animal models provides a rich context in which to investigate the phenotypic impact of these molecules. Promising initial studies using animal models demonstrated that lncRNAs influence a diverse number of phenotypes, ranging from subtle dysmorphia to viability. Here, we highlight the diversity of animal models and their unique advantages, discuss the use of animal models to profile lncRNA expression, evaluate experimental strategies to manipulate lncRNA function in vivo, and review the phenotypes attributable to lncRNAs. Despite a limited number of studies leveraging animal models, lncRNAs are already recognized as a notable class of molecules with important implications for health and disease.
Yadav V.P.,Jawaharlal Nehru University |
Mandal P.K.,Jawaharlal Nehru University |
Mandal P.K.,McKusick Nathans Institute for Genetic Medicine |
Bhattacharya A.,Jawaharlal Nehru University |
Bhattacharya S.,Jawaharlal Nehru University
Nature Communications | Year: 2012
Non-long terminal repeat Retrotransposons are referred to as long interspersed nuclear elements (LINEs) and their non-autonomous partners are short interspersed nuclear elements (SINEs). It is believed that an active SINE copy, upon retrotransposition, generates near identical copies of itself, which subsequently accumulate mutations resulting in sequence polymorphism. Here we show that when a retrotransposition-competent cell line of the parasitic protist Entamoeba histolytica, transfected with a marked SINE copy, is induced to retrotranspose, >20% of the newly retrotransposed copies are neither identical to the marked SINE nor to the mobilized resident SINEs. Rather they are recombinants of resident SINEs and the marked SINE. They are a consequence of retrotransposition and not DNA recombination, as they are absent in cells not expressing the retrotransposition functions. This high-frequency recombination provides a new explanation for the existence of mosaic SINEs, which may impact on genetic analysis of SINE lineages, and measurement of phylogenetic distances. © 2012 Macmillan Publishers Limited. All rights reserved.