GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

Publisher's version (útgefin grein).Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.We are grateful to our colleagues from deCODE genetics / Amgen Inc. for their contributions. We also wish to thank all research participants who provided a biological sample to deCODE genetics.Peer Reviewe

MAP1B mutations cause intellectual disability and extensive white matter deficit

Publisher's version (útgefin grein). Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Discovery of coding variants in genes that confer risk of neurodevelopmental disorders is an important step towards understanding the pathophysiology of these disorders. Wholegenome sequencing of 31,463 Icelanders uncovers a frameshift variant (E712KfsTer10) in microtubule-associated protein 1B (MAP1B) that associates with ID/low IQ in a large pedigree (genome-wide corrected P = 0.022). Additional stop-gain variants in MAP1B (E1032Ter and R1664Ter) validate the association with ID and IQ. Carriers have 24% less white matter (WM) volume (β = −2.1SD, P = 5.1 × 10−8), 47% less corpus callosum (CC) volume (β = −2.4SD, P = 5.5 × 10−10) and lower brain-wide fractional anisotropy (P = 6.7 × 10−4). In summary, we show that loss of MAP1B function affects general cognitive ability through a profound, brain-wide WM deficit with likely disordered or compromised axons.We are grateful to the participants and we thank the psychologists, nurses and staff, in particular Berglind Eiriksdottir, at the Research Recruitment Center and technicians and staff at Röntgen Domus. We also thank the staff at deCODE genetics core facilities and all our colleagues for their important contribution to this work. L.J. received support from the Swedish Society of Medicine, the Swedish Brain Foundation and Swedish Society for Medical Research. The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreements’ no. 115008 (NEWMEDS) and no. 115300 (EUAIMS) of which resources are composed of EFPIA in-kind contribution and financial contribution from the European Union’s Seventh Framework Programme (EU-FP7/2007-2013), EU-FP7 funded grant no. 602450 (IMAGEMEND) and EU funded FP7-People-2011-IAPP grant agreement no. 286213 (PsychDPC).Peer Reviewe

miR-199a expression and its targets during development in different Arctic charr morphs

The four morphs of Arctic charr in Þingvallavatn differ significantly in morphology, especially in their feeding apparatus. Given the evolutionary history of Arctic charr in Iceland it is likely that genes engaged in the formation of the craniofacial structures are expressed differentially between the morphs. miRNAs are known to play an important role in the differentiation and the development of the cartilage. miR-199a is of particular interest because it is highly conserved among vertebrates, exhibits a differential expression pattern in transcriptome data from different Arctic charr morphs and is reported to be specifically expressed in the skeletal system in other vertebrates. To gain a better understanding of the developmental processes miR-199a is involved in, which genes it interacts with and regulates, it is important to identify its mRNA targets. With this in mind the expression of miR-199a was studied during the embryonic development in the head of two Arctic charr morphs, large benthivorous and planktivorous using WISH at three developmental stages (177 DD, 200 DD and 238 DD). miR-199a was expressed in the craniofacial elements at all stages in both morphs and its expression decreased from the earliest to the latest stage as well as showing differences between the morphs. Four candidate mRNA targets were identified with computational approaches. Two of them (lum and ets2) were studied with WISH and showed similar patterns of expression as miR-199a in both morphs at stage 200 DD. miQPCR was also used to determine the expression differences of miR-199a between morphs although without success

Forstökkbreytingar í C9ORF72 og FMR1 á Íslandi

Modern sequencing technology has been instrumental in determining the sequence of DNA. However, there are regions within the genome that cannot be sequenced using traditional methods. Repetitive DNA sequences such as GC-rich repeat expansions can alter gene expression and confer risk of or cause diseases. If these repeats are not fully expanded, they are sometimes called premutations (PM). PM may contribute to neuropsychological and/or neurodegenerative disorders and can mutate to a full mutation (FM). Attaining the number of long repeats has been problematic, especially for a large population based sample. Here, we used a novel approach involving whole genome sequencing, two-primer PCR, and three-primer PCR to determine accurately the repeat number in C9ORF72. We used genotype data together with data from a three-primer PCR to find PM haplotypes in FMR1 and used them to identify PM candidates in the Icelandic population. The varying lengths of the C9ORF72 and FMR1 repeats were then associated with different phenotypes. We detected a significant association between long repeats in C9ORF72 and ALS (p = 5.14×10-7, OR = 86.4). Further, we detected an association with Alzheimer’s disease (p = 5.09×10-5, OR = 16.1). Phenotypes previously associated with the FMR1 PM could not be confirmed in the Icelandic sample. The novel approach used in this study can be used to identify PM carriers of other repeat expansions and estimate their impact in large samples.Raðgreiningartækni hefur spilað mikilvægt hlutverk í að ákvarða röð niturbasanna í erfðamengi mannsins. Það eru þó svæði innan þess sem er ekki hægt að raðgreina með hefðbundnum aðferðum. Langar og GC-ríkar endurtekningar í erfðamenginu eru dæmi um svæði sem erfitt er að raðgreina en slíkar raðir geta breytt tjáningu gena og valdið sjúkdómum. Til eru endurtekningar sem kallast forstökkbreytingar (PM) en þær eru ekki jafn langar og sjúkdómsvaldandi endurtekningar (FM) en geta þó aukið líkur á öðrum röskunum í taugakerfinu. Það hefur verið erfitt að leggja mat á lengd endurtekninganna, sérstaklega í stórum þýðum. Við settum saman nýja aðferð, sem samanstendur af heilraðgreiningu, tveggja-vísa PCR og þriggja-vísa PCR, til að ákvarða fjölda endurtekninga í C9ORF72. Við notuðum arfgerðargögn og þriggja-vísa PCR til að finna setröð sem aðeins fannst í FMR1 PM berum og bárum kennsl á mögulega PM bera í íslensku þjóðinni. Fylgnin milli mismunandi lengdar á endurtekningunum í C9ORF72 og FMR1 og mismunandi svipgerða var skoðuð. Við sáum marktæka fylgni milli langra endurtekninga í C9ORF72 og blandaðrar hreyfitaugahrörnunar (p = 5.14×10-7, OR = 86.4). Við sáum einnig marktækt samband við Alzheimers sjúkdóm (p = 5.09×10-5, OR = 16.1). Fylgnin milli FMR1 PM bera og svipgerða sem hafa áður verið tengdar við PM var ekki staðfest. Með þessari nýju aðferð, sem var notast við í rannsókninni, er hægt að finna PM bera á öðrum löngum endurtekningum og meta áhrif þeirra í stóru þýði

A PRPH splice-donor variant associates with reduced sural nerve amplitude and risk of peripheral neuropathy

Publisher's version (útgefin grein).Nerve conduction (NC) studies generate measures of peripheral nerve function that can reveal underlying pathology due to axonal loss, demyelination or both. We perform a genome-wide association study of sural NC amplitude and velocity in 7045 Icelanders and find a low-frequency splice-donor variant in PRPH (c.996+1G>A; MAF = 1.32%) associating with decreased NC amplitude but not velocity. PRPH encodes peripherin, an intermediate filament (IF) protein involved in cytoskeletal development and maintenance of neurons. Through RNA and protein studies, we show that the variant leads to loss-of-function (LoF), as when over-expressed in a cell line devoid of other IFs, it does not allow formation of the normal filamentous structure of peripherin, yielding instead punctate protein inclusions. Recall of carriers for neurological assessment confirms that from an early age, homozygotes have significantly lower sural NC amplitude than non-carriers and are at risk of a mild, early-onset, sensory-negative, axonal polyneuropathy.We thank all participants in deCODE studies for their valuable contribution to research, especially the participants of the deCODE Health Study and the deCODE Study on Genetics of Chronic and Neuropathic Pain. We also thank the research staff at the Patient Recruitment Center, and all colleagues who contributed to phenotype ascertainment, recruitment, collection of data, sample handling, and genotyping. The financial support from the European Commission to the NeuroPain project (FP7#HEALTH-2013-602891-2) and the National Institutes of Health (R01DE022905) is acknowledged.Peer Reviewe