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Article ; Online: Late diagnosis of a truncating

Alawbathani, Salem / Kawalia, Amit / Karakaya, Mert / Altmüller, Janine / Nürnberg, Peter / Cirak, Sebahattin

Cold Spring Harbor molecular case studies

2018 Volume 4, Issue 1

Abstract: Rare diseases are often misdiagnosed or receive a delayed diagnosis; thus, unfortunately, affected individuals may not receive optimal medical management. Here, we report a case of two siblings with a severe phenotype of progressive pseudorheumatoid ... ...

Abstract	Rare diseases are often misdiagnosed or receive a delayed diagnosis; thus, unfortunately, affected individuals may not receive optimal medical management. Here, we report a case of two siblings with a severe phenotype of progressive pseudorheumatoid dysplasia (PPD). Their onset of symptoms began at the age of 3 yr. Both were neglected in the past, and the patients presented with a very severe phenotype and unmitigated natural history. PPD is a rare autosomal recessive skeletal dysplasia characterized by progressive joint stiffness, swelling, and pain. Because of observed muscle wasting, weakness, and the lack of laboratory testing, the case had been initially misdiagnosed by the local physicians. We aimed to provide diagnostic support by a targeted next-generation sequencing gene panel (Illumina TruSight One) for Mendelian diseases (Mendeliome), and we identified a homozygous frameshift mutation in the gene
MeSH term(s)	Base Sequence ; CCN Intercellular Signaling Proteins/genetics ; Child, Preschool ; Family ; Female ; Humans ; Joint Diseases/diagnosis ; Joint Diseases/diagnostic imaging ; Joint Diseases/genetics ; Joint Diseases/pathology ; Male ; Mutation/genetics ; Pedigree ; Phenotype ; Young Adult
Chemical Substances	CCN Intercellular Signaling Proteins ; CCN6 protein, human
Language	English
Publishing date	2018-02-01
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835759-0
ISSN	2373-2873 ; 2373-2873
ISSN (online)	2373-2873
ISSN	2373-2873
DOI	10.1101/mcs.a002139
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Book ; Online ; Thesis: Addressing NGS Data Challenges: Efficient High Throughput Processing and Sequencing Error Detection

Kawalia, Amit [Verfasser] / Nürnberg, Peter [Gutachter] / Nothnagel, Michael [Gutachter]

2016

Author's details	Amit Kawalia ; Gutachter: Peter Nürnberg, Michael Nothnagel
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universitäts- und Stadtbibliothek Köln
Publishing place	Köln
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Mutational profiling in the peripheral blood leukocytes of patients with systemic mast cell activation syndrome using next-generation sequencing.

Altmüller, Janine / Haenisch, Britta / Kawalia, Amit / Menzen, Markus / Nöthen, Markus M / Fier, Heide / Molderings, Gerhard J

Immunogenetics

2017 Volume 69, Issue 6, Page(s) 359–369

Abstract: Mast cell activation syndrome (MCAS) and systemic mastocytosis (SM) are two clinical systemic mast cell activation disease variants. Few studies to date have investigated the genetic basis of MCAS. The present study had two aims. First, to investigate ... ...

Abstract	Mast cell activation syndrome (MCAS) and systemic mastocytosis (SM) are two clinical systemic mast cell activation disease variants. Few studies to date have investigated the genetic basis of MCAS. The present study had two aims. First, to investigate whether peripheral blood leukocytes from MCAS patients also harbor somatic mutations in genes implicated in SM using next-generation sequencing (NGS) technology and a relatively large MCAS cohort. We also addressed the question, whether some of the previously as somatic reported mutations are indeed germline mutations. Second, to identify germline mutations of relevance to MCAS pathogenesis. Here, mutation frequency in the present MCAS cohort was compared to that in public- and in-house databases in the case of frequent variants, and co-segregation was investigated in multiply affected families in the case of rare variants (allele frequency < 1%). MCAS diagnoses were assigned according to current criteria. Twenty five candidate genes were selected on the basis of published findings for SM. NGS was performed using a 76kbp custom designed Agilent SureSelect Target Enrichment and an Illumina Hiseq2000 2x100bp sequencing run. NGS revealed 67 germline mutations. No somatic mutations were detected. None of the germline mutations showed unequivocal association with MCAS. Failure to detect somatic mutations was probably attributable to the dilution of mutated mast cell DNA in normal leukocyte DNA. The present exploratory association findings suggest that some of the detected germline mutations may be functionally relevant and explain familial aggregation. Independent replication studies are therefore warranted.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Alleles ; Amino Acid Substitution ; Biomarkers ; DNA Mutational Analysis ; Female ; Gene Frequency ; Genome-Wide Association Study ; Genomics/methods ; Germ-Line Mutation ; High-Throughput Nucleotide Sequencing ; Humans ; Leukocytes/metabolism ; Male ; Mastocytosis/diagnosis ; Mastocytosis/genetics ; Middle Aged ; Mutation ; Pedigree ; Phenotype ; Polymorphism, Single Nucleotide ; Syndrome ; Young Adult
Chemical Substances	Biomarkers
Language	English
Publishing date	2017-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	186560-2
ISSN	1432-1211 ; 0093-7711
ISSN (online)	1432-1211
ISSN	0093-7711
DOI	10.1007/s00251-017-0981-y
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Article: Recurrent and Prolonged Infections in a Child with a Homozygous

Zaki, Maha / Thoenes, Michaela / Kawalia, Amit / Nürnberg, Peter / Kaiser, Rolf / Heller, Raoul / Bolz, Hanno J

Frontiers in genetics

2017 Volume 8, Page(s) 130

Abstract: In an Egyptian girl born to consanguineous parents, whole-exome sequencing (WES) identified a homozygous mutation ... ...

Abstract	In an Egyptian girl born to consanguineous parents, whole-exome sequencing (WES) identified a homozygous mutation in
Language	English
Publishing date	2017-09-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2017.00130
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Article ; Online: Novel mutations in

Dafsari, Hormos Salimi / Kawalia, Amit / Sprute, Rosanne / Karakaya, Mert / Malenica, Anna / Herkenrath, Peter / Nürnberg, Peter / Motameny, Susanne / Thiele, Holger / Cirak, Sebahattin

Cold Spring Harbor molecular case studies

2019 Volume 5, Issue 6

Abstract: Infants suffering from life-threatening apnea, stridor, cyanosis, and increased muscle tone may often be misdiagnosed with infantile seizures and inappropriately treated because of lack and delay in genetic diagnosis. Here, we report a patient with ... ...

Abstract	Infants suffering from life-threatening apnea, stridor, cyanosis, and increased muscle tone may often be misdiagnosed with infantile seizures and inappropriately treated because of lack and delay in genetic diagnosis. Here, we report a patient with increased muscle tone after birth and hypertonic attacks with life-threatening apnea but no epileptiform patterns in EEG recordings. We identified novel compound heterozygous variants in
MeSH term(s)	Apnea/genetics ; Child, Preschool ; Glycine Plasma Membrane Transport Proteins/genetics ; Glycine Plasma Membrane Transport Proteins/metabolism ; Humans ; Hyperekplexia/genetics ; Hyperekplexia/therapy ; Infant ; Male ; Mutation ; Whole Exome Sequencing/methods
Chemical Substances	Glycine Plasma Membrane Transport Proteins ; SLC6A5 protein, human
Language	English
Publishing date	2019-12-13
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835759-0
ISSN	2373-2873 ; 2373-2873
ISSN (online)	2373-2873
ISSN	2373-2873
DOI	10.1101/mcs.a004465
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Article ; Online: Comprehensive molecular analysis of 61 Egyptian families with hereditary nonsyndromic hearing loss.

Budde, Birgit S / Aly, Maha Abdelgaber / Mohamed, Mostafa R / Breß, Andreas / Altmüller, Janine / Motameny, Susanne / Kawalia, Amit / Thiele, Holger / Konrad, Kathryn / Becker, Christian / Toliat, Mohammad R / Nürnberg, Gudrun / Sayed, Eman Abdel Fattah / Mohamed, Enass Sayed / Pfister, Markus / Nürnberg, Peter

Clinical genetics

2020 Volume 98, Issue 1, Page(s) 32–42

Abstract: Nonsyndromic hearing loss is an extremely heterogeneous disorder. Thus, clinical diagnostics is challenging, in particular due to differences in the etiology of hearing loss between populations. With this study, we wanted to elucidate the genetic basis ... ...

Abstract	Nonsyndromic hearing loss is an extremely heterogeneous disorder. Thus, clinical diagnostics is challenging, in particular due to differences in the etiology of hearing loss between populations. With this study, we wanted to elucidate the genetic basis of hearing loss in 61 consanguineous Egyptian families. In 25 families, linkage analysis was used as a prescreening to identify regions for targeted sequencing of candidate genes. Initially, the coding regions of 12 and later of 94 genes associated with hearing loss were enriched and subjected to massively parallel sequencing (MPS) with diagnostic yields of 36% and 75%, respectively. Causative variants were identified in 48 families (79%). They were found in 23 different genes with the majority being located in MYO15A (15.3%), SLC26A4 (9.7%), GJB2 (8.3%), and MYO7A (6.4%). As many as 32 variants were novel ones at the time of detection. Five variants were shared by two, three, or even four families. Our study provides a first survey of the mutational spectrum of deaf patients in Egypt revealing less GJB2 variants than in many European populations. It underlines the value of targeted enrichment of well-selected deafness genes in combination with MPS in the diagnostics of this frequent and genetically heterogeneous disorder.
MeSH term(s)	Deafness/genetics ; Egypt ; Family ; Female ; Hearing Loss, Sensorineural/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Pedigree
Language	English
Publishing date	2020-04-23
Publishing country	Denmark
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	221209-2
ISSN	1399-0004 ; 0009-9163
ISSN (online)	1399-0004
ISSN	0009-9163
DOI	10.1111/cge.13754
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Article ; Online: Leveraging the power of high performance computing for next generation sequencing data analysis: tricks and twists from a high throughput exome workflow.

Kawalia, Amit / Motameny, Susanne / Wonczak, Stephan / Thiele, Holger / Nieroda, Lech / Jabbari, Kamel / Borowski, Stefan / Sinha, Vishal / Gunia, Wilfried / Lang, Ulrich / Achter, Viktor / Nürnberg, Peter

PloS one

2015 Volume 10, Issue 5, Page(s) e0126321

Abstract: Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of ... ...

Abstract	Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of data. Complex bioinformatics analyses are required to turn these data into scientific findings. In order to run these analyses fast, automated workflows implemented on high performance computers are state of the art. While providing sufficient compute power and storage to meet the NGS data challenge, high performance computing (HPC) systems require special care when utilized for high throughput processing. This is especially true if the HPC system is shared by different users. Here, stability, robustness and maintainability are as important for automated workflows as speed and throughput. To achieve all of these aims, dedicated solutions have to be developed. In this paper, we present the tricks and twists that we utilized in the implementation of our exome data processing workflow. It may serve as a guideline for other high throughput data analysis projects using a similar infrastructure. The code implementing our solutions is provided in the supporting information files.
MeSH term(s)	Automatic Data Processing/methods ; Computational Biology/methods ; Computing Methodologies ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; Workflow
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0126321
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Article ; Online: Correction: The genomic and clinical landscape of fetal akinesia.

Pergande, Matthias / Motameny, Susanne / Özdemir, Özkan / Kreutzer, Mona / Wang, Haicui / Daimagüler, Hülya-Sevcan / Becker, Kerstin / Karakaya, Mert / Ehrhardt, Harald / Elcioglu, Nursel / Ostojic, Slavica / Chao, Cho-Ming / Kawalia, Amit / Duman, Özgür / Koy, Anne / Hahn, Andreas / Reimann, Jens / Schoner, Katharina / Schänzer, Anne /

Westhoff, Jens H / Schwaibold, Eva Maria Christina / Cossee, Mireille / Imbert-Bouteille, Marion / von Pein, Harald / Haliloglu, Göknur / Topaloglu, Haluk / Altmüller, Janine / Nürnberg, Peter / Thiele, Holger / Heller, Raoul / Cirak, Sebahattin

Genetics in medicine : official journal of the American College of Medical Genetics

2020 Volume 22, Issue 8, Page(s) 1426–1428

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2020-05-25
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1455352-1
ISSN	1530-0366 ; 1098-3600
ISSN (online)	1530-0366
ISSN	1098-3600
DOI	10.1038/s41436-020-0839-9
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Article ; Online: Rare gene deletions in genetic generalized and Rolandic epilepsies.

Jabbari, Kamel / Bobbili, Dheeraj R / Lal, Dennis / Reinthaler, Eva M / Schubert, Julian / Wolking, Stefan / Sinha, Vishal / Motameny, Susanne / Thiele, Holger / Kawalia, Amit / Altmüller, Janine / Toliat, Mohammad Reza / Kraaij, Robert / van Rooij, Jeroen / Uitterlinden, André G / Ikram, M Arfan / Zara, Federico / Lehesjoki, Anna-Elina / Krause, Roland /

Zimprich, Fritz / Sander, Thomas / Neubauer, Bernd A / May, Patrick / Lerche, Holger / Nürnberg, Peter

PloS one

2018 Volume 13, Issue 8, Page(s) e0202022

Abstract: Genetic Generalized Epilepsy (GGE) and benign epilepsy with centro-temporal spikes or Rolandic Epilepsy (RE) are common forms of genetic epilepsies. Rare copy number variants have been recognized as important risk factors in brain disorders. We performed ...

Abstract	Genetic Generalized Epilepsy (GGE) and benign epilepsy with centro-temporal spikes or Rolandic Epilepsy (RE) are common forms of genetic epilepsies. Rare copy number variants have been recognized as important risk factors in brain disorders. We performed a systematic survey of rare deletions affecting protein-coding genes derived from exome data of patients with common forms of genetic epilepsies. We analysed exomes from 390 European patients (196 GGE and 194 RE) and 572 population controls to identify low-frequency genic deletions. We found that 75 (32 GGE and 43 RE) patients out of 390, i.e. ~19%, carried rare genic deletions. In particular, large deletions (>400 kb) represent a higher burden in both GGE and RE syndromes as compared to controls. The detected low-frequency deletions (1) share genes with brain-expressed exons that are under negative selection, (2) overlap with known autism and epilepsy-associated candidate genes, (3) are enriched for CNV intolerant genes recorded by the Exome Aggregation Consortium (ExAC) and (4) coincide with likely disruptive de novo mutations from the NPdenovo database. Employing several knowledge databases, we discuss the most prominent epilepsy candidate genes and their protein-protein networks for GGE and RE.
MeSH term(s)	Autistic Disorder/genetics ; Autistic Disorder/metabolism ; Chromosome Deletion ; Comparative Genomic Hybridization ; DNA Copy Number Variations ; Epilepsy, Generalized/genetics ; Epilepsy, Rolandic/genetics ; Epilepsy, Rolandic/metabolism ; Exome ; Gene Deletion ; Genetic Association Studies/methods ; Genetic Predisposition to Disease ; Humans ; Mutation ; Protein Interaction Mapping ; Protein Interaction Maps ; Reproducibility of Results ; Workflow
Language	English
Publishing date	2018-08-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0202022
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Article ; Online: Alzheimer's disease-associated (hydroxy)methylomic changes in the brain and blood.

Lardenoije, Roy / Roubroeks, Janou A Y / Pishva, Ehsan / Leber, Markus / Wagner, Holger / Iatrou, Artemis / Smith, Adam R / Smith, Rebecca G / Eijssen, Lars M T / Kleineidam, Luca / Kawalia, Amit / Hoffmann, Per / Luck, Tobias / Riedel-Heller, Steffi / Jessen, Frank / Maier, Wolfgang / Wagner, Michael / Hurlemann, René / Kenis, Gunter /

Ali, Muhammad / Del Sol, Antonio / Mastroeni, Diego / Delvaux, Elaine / Coleman, Paul D / Mill, Jonathan / Rutten, Bart P F / Lunnon, Katie / Ramirez, Alfredo / van den Hove, Daniël L A

Clinical epigenetics

2019 Volume 11, Issue 1, Page(s) 164

Abstract: Background: Late-onset Alzheimer's disease (AD) is a complex multifactorial affliction, the pathogenesis of which is thought to involve gene-environment interactions that might be captured in the epigenome. The present study investigated epigenome-wide ... ...

Abstract	Background: Late-onset Alzheimer's disease (AD) is a complex multifactorial affliction, the pathogenesis of which is thought to involve gene-environment interactions that might be captured in the epigenome. The present study investigated epigenome-wide patterns of DNA methylation (5-methylcytosine, 5mC) and hydroxymethylation (5-hydroxymethylcytosine, 5hmC), as well as the abundance of unmodified cytosine (UC), in relation to AD. Results: We identified epigenetic differences in AD patients (n = 45) as compared to age-matched controls (n = 35) in the middle temporal gyrus, pertaining to genomic regions close to or overlapping with genes such as OXT (- 3.76% 5mC, p Conclusions: The implication of genome-wide significant differential methylation of OXT, encoding oxytocin, in two independent cohorts indicates it is a promising target for future studies on early biomarkers and novel therapeutic strategies in AD.
MeSH term(s)	5-Methylcytosine/analogs & derivatives ; 5-Methylcytosine/analysis ; 5-Methylcytosine/blood ; 5-Methylcytosine/metabolism ; Age of Onset ; Aged ; Aged, 80 and over ; Alzheimer Disease/genetics ; Brain Chemistry ; DNA Methylation ; Disease Progression ; Epigenesis, Genetic ; Female ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Male ; Oxytocin/genetics ; Receptors, Nicotinic/genetics ; Temporal Lobe/chemistry
Chemical Substances	CHRNB1 protein, human ; Intracellular Signaling Peptides and Proteins ; RHBDF2 protein, human ; Receptors, Nicotinic ; 5-hydroxymethylcytosine (1123-95-1) ; Oxytocin (50-56-6) ; 5-Methylcytosine (6R795CQT4H)
Language	English
Publishing date	2019-11-27
Publishing country	Germany
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553921-8
ISSN	1868-7083 ; 1868-7075
ISSN (online)	1868-7083
ISSN	1868-7075
DOI	10.1186/s13148-019-0755-5
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