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Meienberg J.,Center for Cardiovascular Genetics and Gene Diagnostics | Zerjavic K.,Center for Cardiovascular Genetics and Gene Diagnostics | Keller I.,University of Bern | Okoniewski M.,Functional Genomics Center Zurich | And 12 more authors.
Nucleic Acids Research | Year: 2015

Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor-and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants. © 2015 The Author(s).


Meienberg J.,Center for Cardiovascular Genetics and Gene Diagnostics | Zerjavic K.,Center for Cardiovascular Genetics and Gene Diagnostics | Keller I.,University of Bern | Okoniewski M.,ETH Zurich | And 9 more authors.
Nucleic acids research | Year: 2015

Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.


PubMed | University of Zürich, ETH Zurich, Swiss Institute of Bioinformatics, University Hospital and 5 more.
Type: Journal Article | Journal: Nucleic acids research | Year: 2015

Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants.


Schoenhoff F.S.,University Hospital Berne | Mueller C.,University Hospital Berne | Czerny M.,University Hospital Berne | Matyas G.,University Hospital Berne | And 4 more authors.
European Journal of Cardio-thoracic Surgery | Year: 2014

objectives: Loeys-Dietz syndrome (LDS) is characterized by acute aortic dissection (AAD) at aortic diameters below thresholds for intervention in patients with Marfan syndrome (MFS). The aim was to evaluate the outcome of LDS patients primarily treated as having MFS. methods: We analysed 68 consecutive patients who underwent surgery between 1995 and 2007 under the assumption of having MFS before retrospectively being screened for LDS when genetic testing became available. These patients were followed up until 2013, and underwent a total of 115 aortic surgeries. results: Genetic testing was performed in 76% of the patients. Sixty per cent of these patients were positive for FBN1 mutations associated with MFS, 20% had no FBN1 mutation and 17% harboured TGFBR1/2 mutations associated with LDS. Mean follow-up was 12.7 ± 7 years. All-cause 30-day, 6-month and 1-year mortality rates were 2.9, 4.4 and 7.3%, respectively. Interestingly, initial presentation with AAD did not differ between LDS and MFS (33 vs 37%, P = 0.48) nor did long-term mortality compared with MFS patients (11 vs 16%, P = 1.0) or within MFS subgroups (FBN1 positive 13%, P = 1.0; FBN1 negative 10%, P = 1.0; not tested 25%, P = 0.62). There was no difference in the need for secondary total arch replacement between LDS and MFS patients (11 vs 14%, P = 1.0), nor within MFS subgroups (FBN1 positive 16%, P = 1.0; FBN1 negative 10%, P = 1.0; not tested 13%, P = 1.0). Total aortic replacement became necessary in 22% of LDS compared with 12% of MFS patients (P = 0.6) and did not differ significantly between MFS subgroups. Conclusions: Although early surgical intervention in LDS is warranted to avoid AAD, the current data suggest that once the diseased segment is repaired, there seems to be no additional burden in terms of mortality or reoperation rate compared with that in MFS patients, with or without confirmed FBN1 mutation. © The Author 2014. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.


Meienberg J.,Center for Cardiovascular Genetics and Gene Diagnostics | Bruggmann R.,Swiss Institute of Bioinformatics | Oexle K.,Center for Cardiovascular Genetics and Gene Diagnostics | Matyas G.,Center for Cardiovascular Genetics and Gene Diagnostics | Matyas G.,University of Zürich
Human Genetics | Year: 2016

Current clinical next-generation sequencing is done by using gene panels and exome analysis, both of which involve selective capturing of target regions. However, capturing has limitations in sufficiently covering coding exons, especially GC-rich regions. We compared whole exome sequencing (WES) with the most recent PCR-free whole genome sequencing (WGS), showing that only the latter is able to provide hitherto unprecedented complete coverage of the coding region of the genome. Thus, from a clinical/technical point of view, WGS is the better WES so that capturing is no longer necessary for the most comprehensive genomic testing of Mendelian disorders. © 2016, The Author(s).


Oexle K.,Center for Cardiovascular Genetics and Gene Diagnostics
Journal of Human Genetics | Year: 2016

The evenness score (E) in next-generation sequencing (NGS) quantifies the homogeneity in coverage of the NGS targets. Here I clarify the mathematical description of E, which is 1 minus the integral from 0 to 1 over the cumulative distribution function F(x) of the normalized coverage x, where normalization means division by the mean, and derive a computationally more efficient formula; that is, 1 minus the integral from 0 to 1 over the probability density distribution f(x) times 1-x. An analogous formula for empirical coverage data is provided as well as fast R command line scripts. This new formula allows for a general comparison of E with the coefficient of variation (=standard deviation σ of normalized data) which is the conventional measure of the relative width of a distribution. For symmetrical distributions, including the Gaussian, E can be predicted closely as 1-σ 2 /2≥E≥1-σ/2 with σ≤1 owing to normalization and symmetry. In case of the log-normal distribution as a typical representative of positively skewed biological data, the analysis yields E≈exp(-σ∗/2) with σ∗ 2 =ln(σ 2 +1) up to large σ (≤3), and E≈1-F(exp(-1)) for very large σ (≥2.5). In the latter kind of rather uneven coverage, E can provide direct information on the fraction of well-covered targets that is not immediately delivered by the normalized σ. Otherwise, E does not appear to have major advantages over σ or over a simple score exp(-σ) based on it. Actually, exp(-σ) exploits a much larger part of its range for the evaluation of realistic NGS outputs. © 2016 The Japan Society of Human Genetics.


Schoenhoff F.S.,University Hospital Berne | Jungi S.,University Hospital Berne | Czerny M.,University Hospital Berne | Roost E.,University Hospital Berne | And 7 more authors.
Circulation | Year: 2013

Background-The aim of the current study was to investigate incidence and causes of surgical interventions in primarily nontreated aortic segments after previous aortic repair in patients with Marfan syndrome. Methods and Results-Retrospective analysis of 86 consecutive Marfan syndrome patients fulfilling Ghent criteria that underwent 136 aortic surgeries and were followed at this institution in the past 15 years. Mean follow-up was 8.8±6.8 y. Thirty-day, 6-month, 1-year, and overall mortality was 3.5%, 5.8%, 7.0%, and 12.8%, respectively. Ninety-two percent of patients initially presented with aortic root, ascending aortic or arch lesions, whereas 8% presented with descending aortic or thoraco-abdominal lesions. Primary presentation was acute aortic dissection (AAD) in 36% (77% type A, 23% type B) and aneurismal disease in 64%. Secondary complete arch replacement had to be performed in only 6% of patients without AAD, but in 36% with AAD (P=0.0005). In patients without AAD, 11% required surgery on primarily nontreated aortic segments (5 of 6 patients experienced type B dissection during follow-up), whereas in patients after AAD, 48% underwent surgery of initially nontreated aortic segments (42% of patients with type A and 86% of those with type B dissection; P=0.0002). Conclusions-The need for surgery in primarily nontreated aortic segments is precipitated by an initial presentation with AAD. Early elective surgery is associated with low mortality and reintervention rates. Type B dissection in patients with Marfan syndrome is associated with a high need for extensive aortic repair, even if the dissection is being considered uncomplicated by conventional criteria. Copyright © 2013 American Heart Association, Inc.


Attenhofer Jost C.H.,Cardiovascular Center Klinik Im Park | Greutmann M.,University of Zürich | Connolly H.M.,Mayo Medical School | Weber R.,University of Zürich | And 5 more authors.
Current Cardiology Reviews | Year: 2014

Thoracic aortic aneurysms can be triggered by genetic disorders such as Marfan syndrome (MFS) and related aortic diseases as well as by inflammatory disorders such as giant cell arteritis or atherosclerosis. In all these conditions, cardiovascular risk factors, such as systemic arterial hypertension, may contribute to faster rate of aneurysm progression. Optimal medical management to prevent progressive aortic dilatation and aortic dissection is unknown. β-blockers have been the mainstay of medical treatment for many years despite limited evidence of beneficial effects. Recently, losartan, an angiotensin II type I receptor antagonist (ARB), has shown promising results in a mouse model of MFS and subsequently in humans with MFS and hence is increasingly used. Several ongoing trials comparing losartan to β -blockers and/or placebo will better define the role of ARBs in the near future. In addition, other medications, such as statins and tetracyclines have demonstrated potential benefit in experimental aortic aneurysm studies. Given the advances in our understanding of molecular mechanisms triggering aortic dilatation and dissection, individualized management tailored to the underlying genetic defect may be on the horizon of individualized medicine. We anticipate that ongoing research will address the question whether such genotype/pathogenesis-driven treatments can replace current phenotype/syndromedriven strategies and whether other forms of aortopathies should be treated similarly. In this work, we review currently used and promising medical treatment options for patients with heritable aortic aneurysmal disorders. © 2014 Bentham Science Publishers.


Okoniewski M.J.,Functional Genomics Center Zurich | Okoniewski M.J.,University of Zürich | Meienberg J.,Center for Cardiovascular Genetics and Gene Diagnostics | Meienberg J.,University of Zürich | And 6 more authors.
BioTechniques | Year: 2013

Herein we present the applicability of single-molecule (PacBio RS) and second-generation sequencing technology (Illumina) to the characterization of large genomic deletions. By testing samples previously characterized using a Sanger approach, our methods determined that both next-generation sequencing platforms were able to identify the position of deletion breakpoints. Our results point out various advantages of next-generation sequencing platforms when characterizing genomic deletions; however, special attention must be dedicated to identical sequences flanking the breakpoints, such as poly(N) motifs.


PubMed | Center for Cardiovascular Genetics and Gene Diagnostics
Type: Journal Article | Journal: Journal of human genetics | Year: 2016

The evenness score (E) in next-generation sequencing (NGS) quantifies the homogeneity in coverage of the NGS targets. Here I clarify the mathematical description of E, which is 1 minus the integral from 0 to 1 over the cumulative distribution function F(x) of the normalized coverage x, where normalization means division by the mean, and derive a computationally more efficient formula; that is, 1 minus the integral from 0 to 1 over the probability density distribution f(x) times 1-x. An analogous formula for empirical coverage data is provided as well as fast R command line scripts. This new formula allows for a general comparison of E with the coefficient of variation (=standard deviation of normalized data) which is the conventional measure of the relative width of a distribution. For symmetrical distributions, including the Gaussian, E can be predicted closely as 1-(2)/2E1-/2 with 1 owing to normalization and symmetry. In case of the log-normal distribution as a typical representative of positively skewed biological data, the analysis yields Eexp(-*/2) with *(2)=ln((2)+1) up to large (3), and E1-F(exp(-1)) for very large (2.5). In the latter kind of rather uneven coverage, E can provide direct information on the fraction of well-covered targets that is not immediately delivered by the normalized . Otherwise, E does not appear to have major advantages over or over a simple score exp(-) based on it. Actually, exp(-) exploits a much larger part of its range for the evaluation of realistic NGS outputs.

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