Somatic mosaicism in a Cornelia de Lange syndrome patient withNIPBLmutation identified by different next generation sequencing approaches

2014 ◽  
Vol 86 (6) ◽  
pp. 595-597 ◽  
Author(s):  
C. Baquero-Montoya ◽  
M.C. Gil-Rodríguez ◽  
D. Braunholz ◽  
M.E. Teresa-Rodrigo ◽  
C. Obieglo ◽  
...  
2020 ◽  
pp. 1-6
Author(s):  
Selma Demir ◽  
Hakan Gürkan ◽  
Veysel Öz ◽  
Sinem Yalçıntepe ◽  
Emine İ. Atlı ◽  
...  

Wiedemann-Steiner syndrome (WDSTS) is a rare autosomal dominant disorder with a variable clinical phenotype including synophrys, hypertelorism, thick eyebrows, long eyelashes, wide nasal bridge, long philtrum, hypertrichosis, growth retardation, and intellectual disability. Cornelia de Lange syndrome (CdLS) is a rare disease characterized by synophrys, long eyelashes, limb abnormalities, generalized hirsutism, growth retardation, and intellectual disability. In both WDSTS and CdLS, the malformations are due to transcriptome disturbance caused by defects in the genes encoding the components of chromatin regulation and transcription process. The overlapping features in these two syndromes may complicate the original diagnosis of a patient. Here, we report on a Wiedemann-Steiner patient found to have a de novo pathogenic <i>KMT2A</i> variation who had been clinically suspected as CdLS. We suggest that targeted next-generation sequencing is a feasible tool for the precise diagnosis of patients who have phenotypically and clinically overlapping features of CdLS and WDSTS.


2020 ◽  
Vol 183 (5) ◽  
pp. 497-504
Author(s):  
Susanne Thiele ◽  
Ralf Werner ◽  
Annika Stubbe ◽  
Olaf Hiort ◽  
Wolfgang Hoeppner

Background: Hypophosphataemic rickets (HR) comprise a clinically and genetically heterogeneous group of conditions, defined by renal-tubular phosphate wasting and consecutive loss of bone mineralisation. X-linked hypophosphataemia (XLH) is the most common form, caused by inactivating dominant mutations in PHEX, a gene encompassing 22 exons located at Xp22.1. XLH is treatable by anti-Fibroblast Growth Factor 23 antibody, while for other forms of HR such as therapy may not be indicated. Therefore, a genetic differentiation of HR is recommended. Objective: To develop and validate a next-generation sequencing panel for HR with special focus on PHEX. Design and methods: We designed an AmpliSeq gene panel for the IonTorrent PGM next-generation platform for PHEX and ten other HR-related genes. For validation of PHEX sequencing 50 DNA-samples from XLH-patients, in whom 42 different mutations in PHEX and 1 structural variation have been proven before, were blinded, anonymised and investigated with the NGS panel. In addition, we analyzed one known homozygous DMP1 mutation and two samples of HR-patients, where no pathogenic PHEX mutation had been detected by conventional sequencing. Results: The panel detected all 42 pathogenic missense/nonsense/splice-site/indel PHEX-mutations and in one the known homozygous DMP1 mutation. In the remaining two patients, we revealed a somatic mosaicism of a PHEX mutation in one; as well as two variations in DMP1 and a very rare compound heterozygous variation in ENPP1 in the second patient. Conclusions: This developed NGS panel is a reliable tool with high sensitivity and specificity for the diagnosis of XLH and related forms of HR.


2011 ◽  
Vol 9 (S1) ◽  
Author(s):  
K Izawa ◽  
R Nishikomori ◽  
N Tanikaze ◽  
MK Saito ◽  
R Goldbach-Mansky ◽  
...  

2019 ◽  
Vol 105 (4) ◽  
pp. 734-746 ◽  
Author(s):  
Samantha N. McNulty ◽  
Michael J. Evenson ◽  
Meagan M. Corliss ◽  
Latisha D. Love-Gregory ◽  
Molly C. Schroeder ◽  
...  

Cancers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2354
Author(s):  
Alexandra Gráf ◽  
Márton Zsolt Enyedi ◽  
Lajos Pintér ◽  
Éva Kriston-Pál ◽  
Gábor Jaksa ◽  
...  

Germline mutations in the BRCA1 and BRCA2 genes are responsible for hereditary breast and ovarian cancer syndrome. Germline and somatic BRCA1/2 mutations may define therapeutic targets and refine cancer treatment options. However, routine BRCA diagnostic approaches cannot reveal the exact time and origin of BRCA1/2 mutation formation, and thus, the fine details of their contribution to tumor progression remain less clear. Here, we establish a diagnostic pipeline using high-resolution microscopy and laser microcapture microscopy to test for BRCA1/2 mutations in the tumor at the single-cell level, followed by deep next-generation sequencing of various tissues from the patient. To demonstrate the power of our approach, here, we describe a detailed single-cell-level analysis of an ovarian cancer patient we found to exhibit constitutional somatic mosaicism of a pathogenic BRCA2 mutation. Employing next-generation sequencing, BRCA2 c.7795G>T, p.(Glu2599Ter) was detected in 78% of reads in DNA extracted from ovarian cancer tissue and 25% of reads in DNA derived from peripheral blood, which differs significantly from the expected 50% of a hereditary mutation. The BRCA2 mutation was subsequently observed at 17–20% levels in the normal ovarian and buccal tissue of the patient. Together, our findings suggest that this mutation occurred early in embryonic development. Characterization of the mosaic mutation at the single-cell level contributes to a better understanding of BRCA mutation formation and supports the concept that the combination of single-cell and next-generation sequencing methods is advantageous over traditional mutational analysis methods. This study is the first to characterize constitutional mosaicism down to the single-cell level, and it demonstrates that BRCA2 mosaicism occurring early during embryogenesis can drive tumorigenesis in ovarian cancer.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jeffrey N. Dudley ◽  
◽  
Celine S. Hong ◽  
Marwan A. Hawari ◽  
Jasmine Shwetar ◽  
...  

Abstract Background The widespread use of next-generation sequencing has identified an important role for somatic mosaicism in many diseases. However, detecting low-level mosaic variants from next-generation sequencing data remains challenging. Results Here, we present a method for Position-Based Variant Identification (PBVI) that uses empirically-derived distributions of alternate nucleotides from a control dataset. We modeled this approach on 11 segmental overgrowth genes. We show that this method improves detection of single nucleotide mosaic variants of 0.01–0.05 variant allele fraction compared to other low-level variant callers. At depths of 600 × and 1200 ×, we observed > 85% and > 95% sensitivity, respectively. In a cohort of 26 individuals with somatic overgrowth disorders PBVI showed improved signal to noise, identifying pathogenic variants in 17 individuals. Conclusion PBVI can facilitate identification of low-level mosaic variants thus increasing the utility of next-generation sequencing data for research and diagnostic purposes.


2015 ◽  
Vol 37 (9) ◽  
pp. 911-915 ◽  
Author(s):  
Takeshi Kato ◽  
Naoya Morisada ◽  
Hiroaki Nagase ◽  
Masahiro Nishiyama ◽  
Daisaku Toyoshima ◽  
...  

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