13 Works

Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

Niina Sandholm, Ronja Hotakainen, Jani K Haukka, Fanny Jansson Sigfrids, Emma H. Dahlström, Anni A. Antikainen, Erkka Valo, Anna Syreeni, Elina Kilpeläinen, Anastasia Kytölä, Aarno Palotie, Valma Harjutsalo, Carol Forsblom, Per-Henrik Groop & on behalf of the FinnDiane Study Group
We analyzed whole-exome (WES) and whole-genome sequencing (WGS) data of 481 and 474 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 79 serum lipid and apolipoprotein phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance spectroscopy.
The available summary statistic include the single variant results, as well as the SKAT and VT results for protein altering and protein truncating variants with a maximum minor allele frequency cutoff of 5%. for...

Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

Niina Sandholm, Ronja Hotakainen, Jani K Haukka, Fanny Jansson Sigfrids, Emma H. Dahlström, Anni A. Antikainen, Erkka Valo, Anna Syreeni, Elina Kilpeläinen, Anastasia Kytölä, Aarno Palotie, Valma Harjutsalo, Carol Forsblom, Per-Henrik Groop & on behalf of the FinnDiane Study Group
We analyzed whole-exome (WES) and whole-genome sequencing (WGS) data of 481 and 474 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 79 serum lipid and apolipoprotein phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance spectroscopy.
The available summary statistic include the single variant results, as well as the SKAT and VT results for protein altering and protein truncating variants with a maximum minor allele frequency cutoff of 5%. for...

Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

Niina Sandholm, Ronja Hotakainen, Jani K. Haukka, Fanny Jansson Sigfrids, Emma H. Dahlström, Anni A. Antikainen, Erkka Valo, Anna Syreeni, Elina Kilpeläinen, Anastasia Kytölä, Aarno Palotie, Valma Harjutsalo, Carol Forsblom & Per-Henrik Groop
Abstract Background Dyslipidemia is a major risk factor for cardiovascular disease, and diabetes impacts the lipid metabolism through multiple pathways. In addition to the standard lipid measurements, apolipoprotein concentrations provide added awareness of the burden of circulating lipoproteins. While common genetic variants modestly affect the serum lipid concentrations, rare genetic mutations can cause monogenic forms of hypercholesterolemia and other genetic disorders of lipid metabolism. We aimed to identify low-frequency protein-altering variants (PAVs) affecting lipoprotein and...

Permutation-based significance analysis reduces the type 1 error rate in bisulphite sequencing data analysis of human umbilical cord blood samples

Essi Laajala, Viivi Halla-aho, Toni Grönroos, Ubaid Ullah Kalim, Mari Vähä-Mäkilä, Mirja Nurmio, Henna Kallionpää, Niina Lietzén, Juha Mykkänen, Omid Rasool, Jorma Toppari, Matej Orešič, Mikael Knip, Riikka Lund, Riitta Lahesmaa & Harri Lähdesmäki
DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn...

Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

Niina Sandholm, Ronja Hotakainen, Jani K Haukka, Fanny Jansson Sigfrids, Emma H. Dahlström, Anni A. Antikainen, Erkka Valo, Anna Syreeni, Elina Kilpeläinen, Anastasia Kytölä, Aarno Palotie, Valma Harjutsalo, Carol Forsblom, Per-Henrik Groop & on behalf of the FinnDiane Study Group
We analyzed whole-exome (WES) and whole-genome sequencing (WGS) data of 481 and 474 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 79 serum lipid and apolipoprotein phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance spectroscopy.
The available summary statistic include the single variant results, as well as the SKAT and VT results for protein altering and protein truncating variants with a maximum minor allele frequency cutoff of 5%. for...

Design Enters the City: Requisites and Points of Friction in Deepening Public Sector Design

Antti Pirinen, Kaisa Savolainen, Sampsa Hyysalo & Tuuli Mattelmäki

Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples

Essi Laajala, Viivi Halla-aho, Toni Grönroos, Ubaid Ullah Kalim, Mari Vähä-Mäkilä, Mirja Nurmio, Henna Kallionpää, Niina Lietzén, Juha Mykkänen, Omid Rasool, Jorma Toppari, Matej Orešič, Mikael Knip, Riikka Lund, Riitta Lahesmaa & Harri Lähdesmäki
DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn...

Additional file 1 of Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

Niina Sandholm, Ronja Hotakainen, Jani K. Haukka, Fanny Jansson Sigfrids, Emma H. Dahlström, Anni A. Antikainen, Erkka Valo, Anna Syreeni, Elina Kilpeläinen, Anastasia Kytölä, Aarno Palotie, Valma Harjutsalo, Carol Forsblom & Per-Henrik Groop
Additional file 1: Supplementary material. A combined document including all supplementary tables (Tables S1-S11), figures (Figs. S1-S7), and code (Text S1).

Permutation-based significance analysis reduces the type 1 error rate in bisulphite sequencing data analysis of human umbilical cord blood samples

Essi Laajala, Viivi Halla-aho, Toni Grönroos, Ubaid Ullah Kalim, Mari Vähä-Mäkilä, Mirja Nurmio, Henna Kallionpää, Niina Lietzén, Juha Mykkänen, Omid Rasool, Jorma Toppari, Matej Orešič, Mikael Knip, Riikka Lund, Riitta Lahesmaa & Harri Lähdesmäki
DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn...

Cancer-related costs should be allocated in a comparable way—benchmarking costs of cancer in Nordic countries 2012–2017

Paulus Torkki, Riikka-Leena Leskelä, Christoffer Bugge, Johanna Eyrun Torfadottir & Sakari Karjalainen
High costs of cancer, and especially the increase in treatment costs, have raised concerns about the financial sustainability of publicly funded health care systems around the world. As cancers get more prevalent with age, treatment costs are expected to keep rising with aging populations. The objective of the study is to analyze the changes in cost of cancer care broken down into separate cost components and outcomes of cancer treatment in the Nordic countries 2012–2017....

Cancer-related costs should be allocated in a comparable way—benchmarking costs of cancer in Nordic countries 2012–2017

Paulus Torkki, Riikka-Leena Leskelä, Christoffer Bugge, Johanna Eyrun Torfadottir & Sakari Karjalainen
High costs of cancer, and especially the increase in treatment costs, have raised concerns about the financial sustainability of publicly funded health care systems around the world. As cancers get more prevalent with age, treatment costs are expected to keep rising with aging populations. The objective of the study is to analyze the changes in cost of cancer care broken down into separate cost components and outcomes of cancer treatment in the Nordic countries 2012–2017....

Additional file 1 of Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

Niina Sandholm, Ronja Hotakainen, Jani K. Haukka, Fanny Jansson Sigfrids, Emma H. Dahlström, Anni A. Antikainen, Erkka Valo, Anna Syreeni, Elina Kilpeläinen, Anastasia Kytölä, Aarno Palotie, Valma Harjutsalo, Carol Forsblom & Per-Henrik Groop
Additional file 1: Supplementary material. A combined document including all supplementary tables (Tables S1-S11), figures (Figs. S1-S7), and code (Text S1).

Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

Niina Sandholm, Ronja Hotakainen, Jani K. Haukka, Fanny Jansson Sigfrids, Emma H. Dahlström, Anni A. Antikainen, Erkka Valo, Anna Syreeni, Elina Kilpeläinen, Anastasia Kytölä, Aarno Palotie, Valma Harjutsalo, Carol Forsblom & Per-Henrik Groop
Abstract Background Dyslipidemia is a major risk factor for cardiovascular disease, and diabetes impacts the lipid metabolism through multiple pathways. In addition to the standard lipid measurements, apolipoprotein concentrations provide added awareness of the burden of circulating lipoproteins. While common genetic variants modestly affect the serum lipid concentrations, rare genetic mutations can cause monogenic forms of hypercholesterolemia and other genetic disorders of lipid metabolism. We aimed to identify low-frequency protein-altering variants (PAVs) affecting lipoprotein and...

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