Kermit: Linkage map guided long read assembly

Background: With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assembly of long reads is still challenging and often results in a large collection of contigs. Dense linkage maps are collections of markers whose location on the genome is approximately known. Therefore they provide long range information that has the potential to greatly aid in de novo assembly. Previously linkage maps have been used to detect misassemblies and to manually order contigs. However, no fully automated tools exist to incorporate linkage maps in assembly but instead large amounts of manual labour is needed to order the contigs into chromosomes. Results: We formulate the genome assembly problem in the presence of linkage maps and present the first method for guided genome assembly using linkage maps. Our method is based on an additional cleaning step added to the assembly. We show that it can simplify the underlying assembly graph, resulting in more contiguous assemblies and reducing the amount of misassemblies when compared to de novo assembly. Conclusions: We present the first method to integrate linkage maps directly into genome assembly. With a modest increase in runtime, our method improves contiguity and correctness of genome assembly.Peer reviewe

Kermit: Guided Long Read Assembly using Coloured Overlap Graphs

With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assembly of long reads is still challenging and often results in a large collection of contigs. Dense linkage maps are collections of markers whose location on the genome is approximately known. Therefore they provide long range information that has the potential to greatly aid in de novo assembly. Previously linkage maps have been used to detect misassemblies and to manually order contigs. However, no fully automated tools exist to incorporate linkage maps in assembly but instead large amounts of manual labour is needed to order the contigs into chromosomes. We formulate the genome assembly problem in the presence of linkage maps and present the first method for guided genome assembly using linkage maps. Our method is based on an additional cleaning step added to the assembly. We show that it can simplify the underlying assembly graph, resulting in more contiguous assemblies and reducing the amount of misassemblies when compared to de novo assembly

Kermit : Guided Long Read Assembly using Coloured Overlap Graphs

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Thymic neuroendocrine tumors in patients with multiple endocrine neoplasia type 1

Objective MEN1 is associated with an increased risk of developing tumors in different endocrine organs. Neuroendocrine tumors of the thymus (TNETs) are very rare but often have an aggressive nature. We evaluated patients with MEN1 and TNET in three university hospitals in Finland. Design/Methods We evaluated patient records of 183 MEN1-patients from three university hospitals between the years 1985-2019 with TNETs. Thymus tumor specimens were classified according to the new WHO 2021 classification of TNET. We collected data on treatments and outcomes of these patients. Results There were six patients (3.3%) with MEN1 and TNET. Five of them had the same common gene mutation occurring in Finland. They originated from common ancestors encompassing two pairs of brothers from sequential generations. The mean age at presentation of TNET was 44.7 +/- 11.9 years. TNET was classified as atypical carcinoid (AC) in five out of six patients. One patient had a largely necrotic main tumor with very few mitoses and another nodule with 25 mitoses per 2 mm(2), qualifying for the 2021 WHO diagnosis of large cell neuroendocrine carcinoma (LCNEC). In our patients, the 5-year survival of the TNET patients was 62.5% and 10-year survival 31.3%. Conclusion In this study, TNETs were observed in one large MEN1 founder pedigree, where an anticipation-like earlier disease onset was observed in the most recent generation. TNET in MEN1 patients is an aggressive disease. The prognosis can be better by systematic screening. We also show that LCNEC can be associated with TNET in MEN1 patients.Peer reviewe

Muuttuva perheenmuodostus – Syyt, seuraukset ja mahdolliset tulevaisuudet (FLUX).

Muuttuva perheenmuodostus – syyt, seuraukset ja mahdolliset tulevaisuudet, FLUX, on konsortiohanke, jota rahoittaa strategisen tutkimuksen neuvosto, STN. FLUX etsii tutkimukseen perustuvia ratkaisuja, joilla voidaan vaikuttaa ja sopeutua syntyvyyden muutoksiin sekä näiden muutosten aiheuttamaan väestön ikääntymisen kiihtymiseen. Tavoitteena on suomalaisen yhteiskunnan sosiaalisen ja taloudellisen kestävyyden parantaminen.FLUX tutkii syntyvyyden ja perheenmuodostuksen dynamiikkaa ja muutoksia ja tuottaa vastauksia (1) muutosten syistä, (2) niiden seurauksista, (3) siitä, miten syntyvyys ja perhedynamiikka ovat yhteydessä sosiaaliseen ja sukupuolten väliseen eriarvoisuuteen ja haasteisiin psykososiaalisessa ja taloudellisessa hyvinvoinnissa ja (4) siitä, miten valtakunnallista ja paikallista sosiaali- ja perhepolitiikkaa voidaan kehittää uusiin yhteiskunnallisiin haasteisiin vastaamiseksi. Monitieteisessä FLUX-konsortiossa työskentelee johtavia tutkijoita väestötieteestä ja muilta aloilta, jotka ovat tärkeitä syntyvyyden muutosten syiden ja seurausten ymmärtämiseksi.Sidosryhmävuorovaikutuksen keinoin FLUX vahvistaa tutkittuun tietoon perustuvaa sosiaali- ja perhepolitiikan päätöksentekoa sen eri vaiheissa ja julkishallinnon eri tasoilla. Järjestötoimijoiden kanssa tehtävä yhteistyö laajentaa FLUXin mahdollisuuksia vaikuttaa asiantuntijatyöhön ja väestöön käytännön tasolla ja FLUXin monikanavainen, laajalle yleisölle suunnattu selkokielinen viestintä tekee tuotetusta tiedosta saavutettavaa kaikille.</p

Young male patients are at elevated risk of developing serious central nervous system complications during acute Puumala hantavirus infection

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Characteristics and Outcomes of 79 Patients with an Insulinoma : A Nationwide Retrospective Study in Finland

Objective. Insulinomas are rare pancreatic tumours. Population-based data on their incidence, clinical picture, diagnosis, and treatment are almost nonexistent. The aim of this study was to clarify these aspects in a nationwide cohort of insulinoma patients diagnosed during three decades. Design and Methods. Retrospective analysis on all adult patients diagnosed with insulinoma in Finland during 1980-2010. Results. Seventy-nine patients were diagnosed with insulinoma over the research period. The median follow-up from diagnosis to last control visit was one (min 0, max 31) year. The incidence increased from 0.5/million/year in the 1980s to 0.9/million/year in the 2000s (p = 0 002). The median diagnostic delay was 13 months and did not change over the study period. The mean age at diagnosis was 52 (SD 16) years. The overall imaging sensitivity improved from 39% in the 1980s to 98% in the 2000s (p <0 001). Seventy- one (90%) of the patients underwent surgery with a curative aim, two (3%) had palliative surgery, and 6 (8%) were inoperable. There were no significant differences in the types of surgical procedures between the 1980s, 1990s, and 2000s; tumour enucleations comprised 43% of the operations, distal pancreatic resections 45%, and pancreaticoduodenectomies 12%, over the whole study period. Of the patients who underwent surgery with a curative aim, 89% had a full recovery. Postoperative complications occurred in half of the patients, but postoperative mortality was rare. Conclusions. The incidence of insulinomas has increased during the past three decades. Despite the improved diagnostic options, diagnostic delay has remained unchanged. To shorten the delay, clinicians should be informed and alert to consider the possibility of hypoglycemia and insulinoma, when symptomatic attacks are investigated in different sectors of the healthcare system. Developing the surgical treatment is another major target, in order to lower the overall complication rate, without compromising the high cure rate of insulinomas.Peer reviewe

The Glanville fritillary genome retains ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

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Characteristics and Outcomes of 79 Patients with an Insulinoma: A Nationwide Retrospective Study in Finland

Objective. Insulinomas are rare pancreatic tumours. Population-based data on their incidence, clinical picture, diagnosis, and treatment are almost nonexistent. The aim of this study was to clarify these aspects in a nationwide cohort of insulinoma patients diagnosed during three decades. Design and Methods. Retrospective analysis on all adult patients diagnosed with insulinoma in Finland during 1980-2010. Results. Seventy-nine patients were diagnosed with insulinoma over the research period. The median follow-up from diagnosis to last control visit was one (min 0, max 31) year. The incidence increased from 0.5/million/year in the 1980s to 0.9/million/year in the 2000s (p = 0 002). The median diagnostic delay was 13 months and did not change over the study period. The mean age at diagnosis was 52 (SD 16) years. The overall imaging sensitivity improved from 39% in the 1980s to 98% in the 2000s (p < 0 001). Seventy- one (90%) of the patients underwent surgery with a curative aim, two (3%) had palliative surgery, and 6 (8%) were inoperable. There were no significant differences in the types of surgical procedures between the 1980s, 1990s, and 2000s; tumour enucleations comprised 43% of the operations, distal pancreatic resections 45%, and pancreaticoduodenectomies 12%, over the whole study period. Of the patients who underwent surgery with a curative aim, 89% had a full recovery. Postoperative complications occurred in half of the patients, but postoperative mortality was rare. Conclusions. The incidence of insulinomas has increased during the past three decades. Despite the improved diagnostic options, diagnostic delay has remained unchanged. To shorten the delay, clinicians should be informed and alert to consider the possibility of hypoglycemia and insulinoma, when symptomatic attacks are investigated in different sectors of the healthcare system. Developing the surgical treatment is another major target, in order to lower the overall complication rate, without compromising the high cure rate of insulinomas

A molecular-based identification resource for the arthropods of Finland

Publisher Copyright: © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.Peer reviewe