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Article: Correction to: Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis.

Wallander, Karin / Thonberg, Håkan / Nilsson, Daniel / Tham, Emma

2021 Volume 19, Issue 1, Page(s) 47

Language	English
Publishing date	2021-11-16
Publishing country	Poland
Document type	Published Erratum
ZDB-ID	2252512-9
ISSN	1897-4287 ; 1731-2302
ISSN (online)	1897-4287
ISSN	1731-2302
DOI	10.1186/s13053-021-00204-y
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Article: Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis.

Wallander, Karin / Thonberg, Håkan / Nilsson, Daniel / Tham, Emma

Hereditary cancer in clinical practice

2021 Volume 19, Issue 1, Page(s) 46

Abstract: Multiple primary cancers, defined as three or more primary tumours, are rare, and there are few genetic studies concerning them. There is a need for increased knowledge on the heritability of multiple primary cancers and genotype-phenotype correlations. ... ...

Abstract	Multiple primary cancers, defined as three or more primary tumours, are rare, and there are few genetic studies concerning them. There is a need for increased knowledge on the heritability of multiple primary cancers and genotype-phenotype correlations. We have performed whole-genome/exome sequencing (WGS/WES) in ten individuals with three or more primary tumours, with no previous findings on standard clinical genetic investigations. In one individual with a clinical diagnosis of MEN1, a likely pathogenic cryptic splice site variant was detected in the MEN1 gene. The variant (c.654C > A) is synonymous but we showed in a cDNA analysis that it affects splicing and leads to a frameshift, with the theoretical new amino acid sequence p.(Gly219Glufs*13). In one individual with metachronous colorectal cancers, ovarian cancer, endometrial cancer and chronic lymphocytic leukaemia, we found a likely pathogenic variant in the MLH1 gene (c.27G > A), and two risk factor variants in the genes CHEK2 and HOXB13. The MLH1 variant is synonymous but has previously been shown to be associated to constitutional low-grade hypermethylation of the MLH1 promoter, and segregates with disease in families with colorectal and endometrial cancer. No pathogenic single nucleotide or structural variants were detected in the remaining eight individuals in the study. The pathogenic variants found by WGS/WES were in genes already sequenced by Sanger sequencing and WES in the clinic, without any findings. We conclude that, in individuals with an unequivocal clinical diagnosis of a specific hereditary cancer syndrome, where standard clinical testing failed to detect a causative variant, re-analysis may lead to a diagnosis.
Language	English
Publishing date	2021-10-28
Publishing country	Poland
Document type	Journal Article
ZDB-ID	2252512-9
ISSN	1897-4287 ; 1731-2302
ISSN (online)	1897-4287
ISSN	1731-2302
DOI	10.1186/s13053-021-00203-z
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Article ; Online: Reduced cone photoreceptor function and subtle systemic manifestations in two siblings with loss of SCLT1.

Grudzinska Pechhacker, Monika K / Molnar, Anna / Pekkola Pacheco, Nadja / Thonberg, Håkan / Querat, Laurence / Birkeldh, Ulrika / Nordgren, Ann / Lindstrand, Anna

Ophthalmic genetics

2023 Volume 45, Issue 1, Page(s) 95–102

Abstract: Background: The sodium channel and clathrin linker 1 gene (: Material and methods: Comprehensive eye examination including fundus images, OCT, color vision, visual fields and electroretinography were performed. Affected individuals were assessed by a ...

Abstract	Background: The sodium channel and clathrin linker 1 gene ( Material and methods: Comprehensive eye examination including fundus images, OCT, color vision, visual fields and electroretinography were performed. Affected individuals were assessed by a pediatrician and a medical geneticist for systemic features of ciliopathy. Investigations included echocardiography, abdominal ultrasonography, blood work-up for diabetes, liver and kidney function. Genetic testing included NGS retinal dystrophy panel, segregation analysis and transcriptome sequencing. Results: Two male children, age 10 and 8 years, were affected with attention deficit hyperactivity disorder (ADHD), obesity and mild photophobia. The ophthalmic exam revealed reduced best-corrected visual acuity (BCVA), strabismus, hyperopia, astigmatism and moderate red-green defects. Milder changes suggesting photoreceptors disease were found on retinal imaging. Electroretinogram confirmed cone photoreceptors dysfunction. Genetic testing revealed a homozygous likely pathogenic, splice-site variant in Conclusions: In this report, we highlight the importance of further extensive diagnostics in patients with unexplained reduced vision, strabismus, refractive errors and ADHD spectrum disorders.
MeSH term(s)	Child ; Humans ; Male ; Retinal Cone Photoreceptor Cells/pathology ; Siblings ; Electroretinography ; Retinal Dystrophies/pathology ; Ciliopathies/pathology ; Phenotype ; Pedigree ; Strabismus ; Mutation ; Sodium Channels
Chemical Substances	SCLT1 protein, human ; Sodium Channels
Language	English
Publishing date	2023-05-29
Publishing country	England
Document type	Journal Article
ZDB-ID	1199279-7
ISSN	1744-5094 ; 0167-6784 ; 1381-6810
ISSN (online)	1744-5094
ISSN	0167-6784 ; 1381-6810
DOI	10.1080/13816810.2023.2215332
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Article ; Online: Transposable element insertions in 1000 Swedish individuals.

Bilgrav Saether, Kristine / Nilsson, Daniel / Thonberg, Håkan / Tham, Emma / Ameur, Adam / Eisfeldt, Jesper / Lindstrand, Anna

PloS one

2023 Volume 18, Issue 7, Page(s) e0289346

Abstract: The majority of rare diseases are genetic, and regardless of advanced high-throughput genomics-based investigations, 60% of patients remain undiagnosed. A major factor limiting our ability to identify disease-causing alterations is a poor understanding ... ...

Abstract	The majority of rare diseases are genetic, and regardless of advanced high-throughput genomics-based investigations, 60% of patients remain undiagnosed. A major factor limiting our ability to identify disease-causing alterations is a poor understanding of the morbid and normal human genome. A major genomic contributor of which function and distribution remain largely unstudied are the transposable elements (TE), which constitute 50% of our genome. Here we aim to resolve this knowledge gap and increase the diagnostic yield of rare disease patients investigated with clinical genome sequencing. To this end we characterized TE insertions in 1000 Swedish individuals from the SweGen dataset and 2504 individuals from the 1000 Genomes Project (1KGP), creating seven population-specific TE insertion databases. Of note, 66% of TE insertions in SweGen were present at >1% in the 1KGP databases, proving that most insertions are common across populations. Focusing on the rare TE insertions, we show that even though ~0.7% of those insertions affect protein coding genes, they rarely affect known disease casing genes (<0.1%). Finally, we applied a TE insertion identification workflow on two clinical cases where disease causing TE insertions were suspected and could verify the presence of pathogenic TE insertions in both. Altogether we demonstrate the importance of TE insertion detection and highlight possible clinical implications in rare disease diagnostics.
MeSH term(s)	Humans ; DNA Transposable Elements/genetics ; Mutagenesis, Insertional ; Rare Diseases/genetics ; Sweden ; Genomics
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0289346
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Article: Predominant Spastic Paraparesis Associated With the D178N Mutation in PRNP.

Thams, Sebastian / Paucar, Martin / Wingård, Louise / Thonberg, Håkan / Smith, Colin / Nennesmo, Inger / Svenningsson, Per

Neurology. Genetics

2021 Volume 7, Issue 6, Page(s) e636

Language	English
Publishing date	2021-11-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2818607-2
ISSN	2376-7839
ISSN	2376-7839
DOI	10.1212/NXG.0000000000000636
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Article: Genome sequencing with comprehensive variant calling identifies structural variants and repeat expansions in a large fraction of individuals with ataxia and/or neuromuscular disorders.

Ek, Marlene / Nilsson, Daniel / Engvall, Martin / Malmgren, Helena / Thonberg, Håkan / Pettersson, Maria / Anderlid, Britt-Marie / Hammarsjö, Anna / Helgadottir, Hafdis T / Arnardottir, Snjolaug / Naess, Karin / Nennesmo, Inger / Paucar, Martin / Hjartarson, Helgi Thor / Press, Rayomand / Solders, Göran / Sejersen, Thomas / Lindstrand, Anna / Kvarnung, Malin

Frontiers in neurology

2023 Volume 14, Page(s) 1170005

Abstract: Introduction: Neuromuscular disorders (NMDs) have a heterogeneous etiology. A genetic diagnosis is key to personalized healthcare and access to targeted treatment for the affected individuals.: Methods: In this study, 861 patients with NMDs were ... ...

Abstract	Introduction: Neuromuscular disorders (NMDs) have a heterogeneous etiology. A genetic diagnosis is key to personalized healthcare and access to targeted treatment for the affected individuals. Methods: In this study, 861 patients with NMDs were analyzed with genome sequencing and comprehensive variant calling including single nucleotide variants, small insertions/deletions (SNVs/INDELs), and structural variants (SVs) in a panel of 895 NMD genes, as well as short tandem repeat expansions (STRs) at 28 loci. In addition, for unsolved cases with an unspecific clinical presentation, the analysis of a panel with OMIM disease genes was added. Results: In the cohort, 27% (232/861) of the patients harbored pathogenic variants, of which STRs and SVs accounted for one-third of the patients (71/232). The variants were found in 107 different NMD genes. Furthermore, 18 pediatric patients harbored pathogenic variants in non-NMD genes. Discussion: Our results highlight that for children with unspecific hypotonia, a genome-wide analysis rather than a disease-based gene panel should be considered as a diagnostic approach. More importantly, our results clearly show that it is crucial to include STR- and SV-analyses in the diagnostics of patients with neuromuscular disorders.
Language	English
Publishing date	2023-05-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564214-5
ISSN	1664-2295
ISSN	1664-2295
DOI	10.3389/fneur.2023.1170005
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Article ; Online: Confirmation of high frequency of C9orf72 mutations in patients with frontotemporal dementia from Sweden.

Öijerstedt, Linn / Chiang, Huei-Hsin / Björkström, Jenny / Forsell, Charlotte / Lilius, Lena / Lindström, Anna-Karin / Thonberg, Håkan / Graff, Caroline

Neurobiology of aging

2019 Volume 84, Page(s) 241.e21–241.e25

Abstract: Frontotemporal dementia (FTD) is the second most common early-onset dementia. Up to half of the cases are familial, and several mutations have been identified as pathogenic. Repeat expansion mutations in C9orf72 are the most common genetic cause of FTD ... ...

Abstract	Frontotemporal dementia (FTD) is the second most common early-onset dementia. Up to half of the cases are familial, and several mutations have been identified as pathogenic. Repeat expansion mutations in C9orf72 are the most common genetic cause of FTD and are particularly frequent in Sweden and Finland. We aimed to determine the mutation frequency in patients with FTD ascertained at a memory clinic in Sweden and assess the inheritance pattern in the families. We screened 132 patients with FTD for mutations in C9orf72, GRN, and MAPT, and the frequency was 34.1%. Two novel variations, not previously published, were found; a pathogenic GRN mutation and a MAPT variation in intron 9 that we report as VUS. The likelihood of finding a mutation was highest in patients with a clear family history of dementia or motor neuron disease (76%), but mutations were also found in apparent sporadic cases. This confirms that FTD cohorts from Sweden have a relatively higher risk of an underlying mutation in all risk categories compared with other reported cohorts.
MeSH term(s)	C9orf72 Protein/genetics ; Frontotemporal Dementia/genetics ; Humans ; Mutation ; Porphyria, Acute Intermittent
Chemical Substances	C9orf72 Protein ; C9orf72 protein, human
Language	English
Publishing date	2019-03-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2019.03.009
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Zs.A 1685: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: No common founder for C9orf72 expansion mutation in Sweden.

Chiang, Huei-Hsin / Forsell, Charlotte / Lindström, Anna-Karin / Lilius, Lena / Thonberg, Håkan / Nennesmo, Inger / Graff, Caroline

Journal of human genetics

2017 Volume 62, Issue 2, Page(s) 321–324

Abstract: Hexanucleotide expansion mutations in the chromosome 9 open reading frame 72 (C9orf72) gene is the most common genetic cause for frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). SNP haplotype analyses have suggested that all C9orf72 ...

Abstract	Hexanucleotide expansion mutations in the chromosome 9 open reading frame 72 (C9orf72) gene is the most common genetic cause for frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). SNP haplotype analyses have suggested that all C9orf72 expansion mutations originate from a common founder. However, not all C9orf72 expansion mutation carriers have the same haplotype. To investigate if the C9orf72 expansion mutation carriers in Sweden share a common founder, we have genotyped SNPs flanking the C9orf72 expansion mutation in cases with FTD, FTD-ALS or ALS to perform haplotype analysis. We have genotyped 57 SNPs in 232 cases of which 45 carried the C9orf72 expansion mutation. Two risk haplotypes consisting of 31 SNPs, spanning 131 kbp, were found to be significantly associated with the mutation. In summary, haplotype analysis on Swedish C9orf72 expansion mutation carriers indicates that the C9orf72 expansion mutation arose on at least two risk haplotypes.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Amyotrophic Lateral Sclerosis/genetics ; C9orf72 Protein ; DNA Repeat Expansion/genetics ; Female ; Frontotemporal Dementia/genetics ; Haplotypes/genetics ; Humans ; Male ; Middle Aged ; Polymorphism, Single Nucleotide/genetics ; Proteins/genetics ; Sweden
Chemical Substances	C9orf72 Protein ; C9orf72 protein, human ; Proteins
Language	English
Publishing date	2017-02
Publishing country	England
Document type	Journal Article
ZDB-ID	1425192-9
ISSN	1435-232X ; 1434-5161
ISSN (online)	1435-232X
ISSN	1434-5161
DOI	10.1038/jhg.2016.108
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Article ; Online: The effects of different familial Alzheimer's disease mutations on APP processing in vivo.

Thordardottir, Steinunn / Kinhult Ståhlbom, Anne / Almkvist, Ove / Thonberg, Håkan / Eriksdotter, Maria / Zetterberg, Henrik / Blennow, Kaj / Graff, Caroline

Alzheimer's research & therapy

2017 Volume 9, Issue 1, Page(s) 9

Abstract: Background: Disturbed amyloid precursor protein (APP) processing is considered to be central to the pathogenesis of Alzheimer's disease (AD). The autosomal dominant form of the disease, familial AD (FAD), may serve as a model for the sporadic form of AD. ...

Abstract	Background: Disturbed amyloid precursor protein (APP) processing is considered to be central to the pathogenesis of Alzheimer's disease (AD). The autosomal dominant form of the disease, familial AD (FAD), may serve as a model for the sporadic form of AD. In FAD the diagnosis of AD is reliable and presymptomatic individuals carrying FAD mutations can give valuable insights into the earliest stages of the disease where therapeutic interventions are thought to be the most effective. Methods: In the current cross-sectional study, products of APP processing (e.g., sAPPα, sAPPβ, Aβ Results: We observed pathological APP processing in presymptomatic carriers of FAD mutations, with different profiles of APP and Aβ isoforms in the three mutation carrier groups, APPswe (p.KM670/671NL), APParc (p.E693G) and PSEN1 (p.H163Y), except for the well-established decrease in CSF Aβ Conclusions: These findings add to the current evidence that AD pathophysiology differs between disease-causing mutations and can be monitored in the presymptomatic disease stage by CSF analyses. This may also be important from a therapeutic standpoint, by opening a window to monitor effects of disease-modifying drugs on AD pathophysiology.
MeSH term(s)	Alzheimer Disease/genetics ; Alzheimer Disease/metabolism ; Amyloid beta-Protein Precursor/genetics ; Amyloid beta-Protein Precursor/metabolism ; Apolipoproteins E/genetics ; Cross-Sectional Studies ; Family ; Heterozygote ; Humans ; Middle Aged ; Mutation ; Presenilin-1/genetics
Chemical Substances	Amyloid beta-Protein Precursor ; Apolipoproteins E ; PSEN1 protein, human ; Presenilin-1
Language	English
Publishing date	2017-02-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2506521-X
ISSN	1758-9193 ; 1758-9193
ISSN (online)	1758-9193
ISSN	1758-9193
DOI	10.1186/s13195-017-0234-1
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Article ; Online: Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient

Schoumans Jacqueline / Björkström Jenny / Fallström Marie / Thonberg Håkan / Nennesmo Inger / Graff Caroline

BMC Research Notes, Vol 4, Iss 1, p

2011 Volume 476

Abstract: Abstract Background Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene ... ...

Abstract	Abstract Background Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. Methods We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. Results In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. Conclusions This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus.
Keywords	Medicine ; R ; Biology (General) ; QH301-705.5 ; Science (General) ; Q1-390
Subject code	616
Language	English
Publishing date	2011-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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