| 1. |
- Fang, Li Tai, et al.
(författare)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Tidskriftsartikel (refereegranskat)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 2. |
- Guerriero, Giuseppe, et al.
(författare)
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Efficacy of transcutaneous vagus nerve stimulation as treatment for depression: A systematic review
- 2021
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Ingår i: Journal of Affective Disorders Reports. - : Elsevier BV. - 2666-9153. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Background: Transcutaneous vagus nerve stimulation (tVNS) has been suggested as a treatment method for depression. Methods: A systematic review to systematically evaluate the efficacy of tVNS for the treatment of depression was conducted according to PRISMA guidelines. Primary outcomes were mortality, self-harm, depressive symptoms, and health-related quality of life (HRQoL). Secondary outcomes were anxiety symptoms, medication use, everyday functioning, complications, and patients’ experiences of treatment. Five databases were searched systematically. The included articles were critically appraised and certainty of evidence was assessed using GRADE. Results: Two studies evaluating efficacy and a case series collecting data on complications were included. One randomized trial (n = 37) and one cohort study (n = 160) comparing tVNS with sham-tVNS reported significant reduction in the tVNS group of self-rated (SMD = -0.82, 95%-CI = -1.50, -0.15) but not clinician-rated depressive symptoms, after two weeks, and of both self-rated (SMD = -0.99, 95%-CI = -1.32, -0.66) and clinician-rated (SMD = -0.89, 95%-CI = -1.22, -0.57) depressive symptoms, after four weeks, respectively. Furthermore, the cohort study found reduction of both self-rated (SMD = -0.66, 95%-CI = -0.98, -0.34) and clinician-rated (SMD = -0.14, 95%-CI = -0.46, 0.17) anxiety symptoms. One case series (n = 12), collecting data on complications, reported mild to moderate transient side effects. Limitations: Available studies are few and heterogeneous, have major study limitations, problems with directness and imprecision. Conclusions: It is uncertain whether tVNS reduces depressive symptoms and anxiety. Although existing studies show promising results, further studies are needed to increase the certainty of evidence. © 2021 The Authors
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| 3. |
- Xiao, Wenming, et al.
(författare)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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