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Article ; Online: Statistical genetics and polygenic risk score for precision medicine

Takahiro Konuma / Yukinori Okada

Inflammation and Regeneration, Vol 41, Iss 1, Pp 1-

2021 Volume 5

Abstract: Abstract The prediction of disease risks is an essential part of personalized medicine, which includes early disease detection, prevention, and intervention. The polygenic risk score (PRS) has become the standard for quantifying genetic liability in ... ...

Abstract	Abstract The prediction of disease risks is an essential part of personalized medicine, which includes early disease detection, prevention, and intervention. The polygenic risk score (PRS) has become the standard for quantifying genetic liability in predicting disease risks. PRS utilizes single-nucleotide polymorphisms (SNPs) with genetic risks elucidated by genome-wide association studies (GWASs) and is calculated as weighted sum scores of these SNPs with genetic risks using their effect sizes from GWASs as their weights. The utilities of PRS have been explored in many common diseases, such as cancer, coronary artery disease, obesity, and diabetes, and in various non-disease traits, such as clinical biomarkers. These applications demonstrated that PRS could identify a high-risk subgroup of these diseases as a predictive biomarker and provide information on modifiable risk factors driving health outcomes. On the other hand, there are several limitations to implementing PRSs in clinical practice, such as biased sensitivity for the ethnic background of PRS calculation and geographical differences even in the same population groups. Also, it remains unclear which method is the most suitable for the prediction with high accuracy among numerous PRS methods developed so far. Although further improvements of its comprehensiveness and generalizability will be needed for its clinical implementation in the future, PRS will be a powerful tool for therapeutic interventions and lifestyle recommendations in a wide range of diseases. Thus, it may ultimately improve the health of an entire population in the future.
Keywords	Statistical genomics ; Genome-wide association study ; Polygenic risk score ; Precision medicine ; Pathology ; RB1-214
Subject code	610
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Determining the immune environment of cutaneous T-cell lymphoma lesions through the assessment of lesional blood drops

Kan Torii / Yukinori Okada / Akimichi Morita

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 12

Abstract: Abstract Detailed analysis of the cells that infiltrate lesional skin cannot be performed in skin biopsy specimens using immunohistochemistry or cell separation techniques because enzyme treatments applied during the isolation step can destroy small ... ...

Abstract	Abstract Detailed analysis of the cells that infiltrate lesional skin cannot be performed in skin biopsy specimens using immunohistochemistry or cell separation techniques because enzyme treatments applied during the isolation step can destroy small amounts of protein and minor cell populations in the biopsy specimen. Here, we describe a method for isolating T cells from drops of whole blood obtained from lesions during skin biopsy in patients with cutaneous T-cell lymphoma. Lesional blood is assumed to contain lesional resident cells, cells from capillary vessels, and blood overflowing from capillary vessels into the lesion area. The lesional blood showed substantial increases in distinct cell populations, chemokines, and the expression of various genes. The proportion of CD8+CD45RO+ T cells in the lesional blood negatively correlated with the modified severity-weighted assessment tool scores. CD4+CD45RO+ T cells in the lesional blood expressed genes associated with the development of cancer and progression of cutaneous T-cell lymphoma. In addition, CD8+CD45RO+ T cells in lesional blood had unique T-cell receptor repertoires in lesions of each stage. Assessment of lesional blood drops might provide new insight into the pathogenesis of mycosis fungoides and facilitate evaluation of the treatment efficacy for mycosis fungoides as well as other skin inflammatory diseases.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of position and volume of spaceoccupying liver lesions on liver function index in 99mTc-GSA scintigraphy.

Tokorodani, Ryotaro / Daisaki, Hiromitsu / Yukinori, Okada / Eisuke, Yasuda

Nuclear medicine review. Central & Eastern Europe

2021 Volume 24, Issue 1, Page(s) 1–10

Abstract: Background: The authors aimed to elucidate the effect of liver space-occupying lesions (SOL) on the quantitative index of the hepatic reserve, calculated using the dynamic planar image (LHLplanar), and a three-dimensional quantitative index (LHLSPECT) ... ...

Abstract	Background: The authors aimed to elucidate the effect of liver space-occupying lesions (SOL) on the quantitative index of the hepatic reserve, calculated using the dynamic planar image (LHLplanar), and a three-dimensional quantitative index (LHLSPECT) calculated using quantitative combined modality single-photon emission computed tomography (SPECT/CT). Material and methods: Water balloons of different volumes that simulated liver SOL were placed in various positions in the combined cardiac-liver phantom to examine the effects of liver SOL on visualization and quantitative indicators (LHLplanar and LHLSPECT). A 200 mL water balloon was placed in the anterior right, posterior right, left medial and left lateral lobes in the liver phantom to compare LHLplanar and LHLSPECT values with and without liver SOL at each position. Subsequently, volumes of those in the front of the right lobe were changed to 50 mL, 100 mL, 200 mL, and 400 mL, followed by statistically comparing LHLplanar and LHLSPECT values in the presence and absence of liver SOL. Results: Despite the variation in the degree of defect accumulation with the location of the balloon when using frontal planar imaging, quantitative SPECT/CT imaging identified all defects. Multiple comparison analysis revealed that unlike LHLSPECT, the LHLplanar values changed according to liver SOL position and volume. Conclusions: Liver SOL position and volume may affect the hepatic reserve assessments performed using LHLplanar values. In contrast, LHLSPECT is calculated using quantitative SPECT/CT and considers the effects of scattering and attenuation corrections. Therefore, LHLSPECT is a more accurate quantitative indicator of hepatic reserve than LHLplanar and is expected to facilitate future clinical research.
MeSH term(s)	Female ; Humans ; Liver/diagnostic imaging ; Liver/physiopathology ; Male ; Middle Aged ; Single Photon Emission Computed Tomography Computed Tomography ; Technetium Tc 99m Aggregated Albumin ; Technetium Tc 99m Pentetate
Chemical Substances	Technetium Tc 99m Aggregated Albumin ; technetium Tc 99m DTPA-galactosyl-human serum albumin ; Technetium Tc 99m Pentetate (VW78417PU1)
Language	English
Publishing date	2021-02-12
Publishing country	Poland
Document type	Journal Article
ZDB-ID	1467537-7
ISSN	1644-4345 ; 1506-9680
ISSN (online)	1644-4345
ISSN	1506-9680
DOI	10.5603/NMR.2021.0001
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Article ; Online: A retrospective observational study investigating the factors associated with right heart failure in patients with primary acute pulmonary embolism and deep vein thrombosis

Satoshi Kobayashi / Makoto Muto / Hitoshi Yabe / Masashi Imao / Yukinori Okada

Journal of General and Family Medicine, Vol 21, Iss 3, Pp 63-

2020 Volume 70

Abstract: Abstract Background The relationship between the risk of right heart failure in primary acute pulmonary embolism after embolization and the residual thrombus sites in the pelvis and lower limbs is not clear. Methods This single‐center retrospective ... ...

Abstract	Abstract Background The relationship between the risk of right heart failure in primary acute pulmonary embolism after embolization and the residual thrombus sites in the pelvis and lower limbs is not clear. Methods This single‐center retrospective observational study examined the results of contrast‐enhanced computed tomography and venous ultrasonography of patients with primary acute PE and DVT. We assessed the association between the occurrence of right heart failure and age; gender; pulmonary thrombosis distribution; most proximal site of deep vein thrombosis in the soleal vein, inferior vena cava (IVC), or common iliac vein (CIV); DVT distribution; and malignancy using univariate and multivariate logistic regression. Results In all, 77 of 165 patients were male (mean age: 65.1 ± 13.7 years). Right heart failure occurred in 53 patients (32.1%). Multivariate analysis revealed that the odds ratio (OR) for right heart failure was significantly lower in patients with the most proximal site of DVT in the IVC/CIV (OR = 0.07, 95% confidence interval [CI] 0.01‐0.62, P = .017), while it was significantly higher in females (OR = 2.51, 95% CI 1.05‐6.01, P = .039), and in patients who exhibited the presence of bilateral venous thrombosis (OR = 3.89, 95% CI 1.60‐9.48, P = .003). Conclusion A significant factor involved in PE without right heart failure was the most proximal site of DVT in the IVC/CIV, and significant risk factors associated with PE with right heart failure were more prevalent in females and in patients who exhibited the presence of bilateral venous thrombosis.
Keywords	CT pulmonary angiography ; deep vein thrombosis ; indirect CT venography ; pulmonary embolism ; right heart failure ; ultrasonography ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes

Tatsuhiko Naito / Ken Suzuki / Jun Hirata / Yoichiro Kamatani / Koichi Matsuda / Tatsushi Toda / Yukinori Okada

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 14

Abstract: Human leukocyte antigen (HLA) genes contribute to risk of many complex traits, yet understanding inter-ethnic heterogeneity is computationally challenging. Here, the authors develop DEEP*HLA for imputation of HLA genotypes and show its ability to ... ...

Abstract	Human leukocyte antigen (HLA) genes contribute to risk of many complex traits, yet understanding inter-ethnic heterogeneity is computationally challenging. Here, the authors develop DEEP*HLA for imputation of HLA genotypes and show its ability to disentangle HLA variant risk effects in diverse populations.
Keywords	Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome-wide association study reveals BET1L associated with survival time in the 137,693 Japanese individuals

Masato Akiyama / Saori Sakaue / Atsushi Takahashi / Kazuyoshi Ishigaki / Makoto Hirata / Koichi Matsuda / Yukihide Momozawa / Yukinori Okada / Toshiharu Ninomiya / The Biobank Japan project / Chikashi Terao / Yoshinori Murakami / Michiaki Kubo / Yoichiro Kamatani

Communications Biology, Vol 6, Iss 1, Pp 1-

2023 Volume 7

Abstract: A genome-wide association study in the BioBank Japan cohort reveals new locus, BET1L, which is associated with survival time in a Japanese population. ...

Abstract	A genome-wide association study in the BioBank Japan cohort reveals new locus, BET1L, which is associated with survival time in a Japanese population.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Single-cell multi-omics analysis identifies two distinct phenotypes of newly-onset microscopic polyangiitis

Masayuki Nishide / Kei Nishimura / Hiroaki Matsushita / Ryuya Edahiro / Sachi Inukai / Hiroshi Shimagami / Shoji Kawada / Yasuhiro Kato / Takahiro Kawasaki / Kohei Tsujimoto / Hokuto Kamon / Ryusuke Omiya / Yukinori Okada / Kunihiro Hattori / Masashi Narazaki / Atsushi Kumanogoh

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract The immunological basis of the clinical heterogeneity in autoimmune vasculitis remains poorly understood. In this study, we conduct single-cell transcriptome analyses on peripheral blood mononuclear cells (PBMCs) from newly-onset patients with ... ...

Abstract	Abstract The immunological basis of the clinical heterogeneity in autoimmune vasculitis remains poorly understood. In this study, we conduct single-cell transcriptome analyses on peripheral blood mononuclear cells (PBMCs) from newly-onset patients with microscopic polyangiitis (MPA). Increased proportions of activated CD14+ monocytes and CD14+ monocytes expressing interferon signature genes (ISGs) are distinctive features of MPA. Patient-specific analysis further classifies MPA into two groups. The MPA-MONO group is characterized by a high proportion of activated CD14+ monocytes, which persist before and after immunosuppressive therapy. These patients are clinically defined by increased monocyte ratio in the total PBMC count and have a high relapse rate. The MPA-IFN group is characterized by a high proportion of ISG+ CD14+ monocytes. These patients are clinically defined by high serum interferon-alpha concentrations and show good response to immunosuppressive therapy. Our findings identify the immunological phenotypes of MPA and provide clinical insights for personalized treatment and accurate prognostic prediction.
Keywords	Science ; Q
Subject code	610
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis

Go Sato / Yuya Shirai / Shinichi Namba / Ryuya Edahiro / Kyuto Sonehara / Tsuyoshi Hata / Mamoru Uemura / the Biobank Japan Project / Koichi Matsuda / Yuichiro Doki / Hidetoshi Eguchi / Yukinori Okada

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 11

Abstract: Abstract Integrating genomic data of multiple cancers allows de novo cancer grouping and elucidating the shared genetic basis across cancers. Here, we conduct the pan-cancer and cross-population genome-wide association study (GWAS) meta-analysis and ... ...

Abstract	Abstract Integrating genomic data of multiple cancers allows de novo cancer grouping and elucidating the shared genetic basis across cancers. Here, we conduct the pan-cancer and cross-population genome-wide association study (GWAS) meta-analysis and replication studies on 13 cancers including 250,015 East Asians (Biobank Japan) and 377,441 Europeans (UK Biobank). We identify ten cancer risk variants including five pleiotropic associations (e.g., rs2076295 at DSP on 6p24 associated with lung cancer and rs2525548 at TRIM4 on 7q22 nominally associated with six cancers). Quantifying shared heritability among the cancers detects positive genetic correlations between breast and prostate cancer across populations. Common genetic components increase the statistical power, and the large-scale meta-analysis of 277,896 breast/prostate cancer cases and 901,858 controls identifies 91 newly genome-wide significant loci. Enrichment analysis of pathways and cell types reveals shared genetic backgrounds across said cancers. Focusing on genetically correlated cancers can contribute to enhancing our insights into carcinogenesis.
Keywords	Science ; Q
Subject code	616
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data

Toshihiro Kishikawa / Yukihide Momozawa / Takeshi Ozeki / Taisei Mushiroda / Hidenori Inohara / Yoichiro Kamatani / Michiaki Kubo / Yukinori Okada

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 10

Abstract: Abstract In the design of whole-genome sequencing (WGS) studies, sequencing depth is a crucial parameter to define variant calling accuracy and study cost, with no standard recommendations having been established. We empirically evaluated the variant ... ...

Abstract	Abstract In the design of whole-genome sequencing (WGS) studies, sequencing depth is a crucial parameter to define variant calling accuracy and study cost, with no standard recommendations having been established. We empirically evaluated the variant calling accuracy of the WGS pipeline using ultra-deep WGS data (approximately 410×). We randomly sampled sequence reads and constructed a series of simulation WGS datasets with a variety of gradual depths (n = 54; from 0.05× to 410×). Next, we evaluated the genotype concordances of the WGS data with those in the SNP microarray data or the WGS data using all the sequence reads. In addition, we assessed the accuracy of HLA allele genotyping using the WGS data with multiple software tools (PHLAT, HLA-VBseq, HLA-HD, and SNP2HLA). The WGS data with higher depths showed higher concordance rates, and >13.7× depth achieved as high as >99% of concordance. Comparisons with the WGS data using all the sequence reads showed that SNVs achieved >95% of concordance at 17.6× depth, whereas indels showed only 60% concordance. For the accuracy of HLA allele genotyping using the WGS data, 13.7× depth showed sufficient accuracy while performance heterogeneity among the software tools was observed (the highest concordance of 96.9% was observed with HLA-HD). Improvement in HLA genotyping accuracy by further increasing the depths was limited. These results suggest a medium degree of the WGS depth setting (approximately 15×) to achieve both accurate SNV calling and cost-effectiveness, whereas relatively higher depths are required for accurate indel calling.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-02-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Serum KL-6 levels predict clinical outcomes and are associated with MUC1 polymorphism in Japanese patients with COVID-19

Takanori Kanai / Yukinori Okada / Yasunori Sato / Katsunori Masaki / Takanori Asakura / Kaori Sakurai / Yuko Kitagawa / Koichi Fukunaga / Hirofumi Kamata / Makoto Ishii / Naoki Hasegawa / Ryuji Koike / Ho Lee / Ryuya Edahiro / Shotaro Chubachi / Kensuke Nakagawara / Ho Namkoong / Hiromu Tanaka / Seiya Imoto /

Shuhei Azekawa / Shiro Otake / Takahiro Fukushima / Mayuko Watase / Tatsuya Kusumoto / Akinori Kimura / Satoru Miyano / Seishi Ogawa

BMJ Open Respiratory Research, Vol 10, Iss

2023 Volume 1

Abstract: Background Krebs von den Lungen-6 (KL-6) is a known biomarker for diagnosis and monitoring of interstitial lung diseases. However, the role of serum KL-6 and the mucin 1 (MUC1) variant (rs4072037) in COVID-19 outcomes remains to be elucidated. We aimed ... ...

Abstract	Background Krebs von den Lungen-6 (KL-6) is a known biomarker for diagnosis and monitoring of interstitial lung diseases. However, the role of serum KL-6 and the mucin 1 (MUC1) variant (rs4072037) in COVID-19 outcomes remains to be elucidated. We aimed to evaluate the relationships among serum KL-6 levels, critical outcomes and the MUC1 variant in Japanese patients with COVID-19.Methods This is a secondary analysis of a multicentre retrospective study using data from the Japan COVID-19 Task Force collected from February 2020 to November 2021, including 2226 patients with COVID-19 whose serum KL-6 levels were measured. An optimal serum KL-6 level cut-off to predict critical outcomes was determined and used for multivariable logistic regression analysis. Furthermore, the relationship among the allele dosage of the MUC1 variant, calculated from single nucleotide polymorphism typing data of genome-wide association studies using the imputation method, serum KL-6 levels and COVID-19 critical outcomes was evaluated.Results Serum KL-6 levels were significantly higher in patients with COVID-19 with critical outcomes (511±442 U/mL) than those without (279±204 U/mL) (p<0.001). Serum KL-6 levels ≥304 U/mL independently predicted critical outcomes (adjusted OR (aOR) 3.47, 95% CI 2.44 to 4.95). Moreover, multivariable logistic regression analysis with age and sex indicated that the MUC1 variant was independently associated with increased serum KL-6 levels (aOR 0.24, 95% CI 0.28 to 0.32) but not significantly associated with critical outcomes (aOR 1.11, 95% CI 0.80 to 1.54).Conclusion Serum KL-6 levels predicted critical outcomes in Japanese patients with COVID-19 and were associated with the MUC1 variant. Therefore, serum KL-6 level is a potentially useful biomarker of critical COVID-19 outcomes.
Keywords	Medicine ; R ; Diseases of the respiratory system ; RC705-779
Subject code	610
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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