Additional file 1 of Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma

Additional file 1: Fig. S1. The performance comparison of four tools in detecting Indels. Fig. S2. The IGV plot of ten non-ref NUMTs. Fig. S3. The IGV plot of the most confident non-ref NUMT detected by NUMTs-detection. Fig. S4. The circos plots of non-ref NUMTs of different sizes and origins. Fig. S5. The IGV plot and the alignment of the inserted sequences extracted from the long-read sequencing data. Fig. S6. The filtering of variants inside the mtDNA NUMT segments. Fig. S7. The correlation between the number of variants per sample and mitochondrial depth under different VAFs before and after mtDNA copy number-based filter. Fig. S8. The 96 mutational contexts of SNVs of all samples. Fig. S9. The mutational spectrum of SNVs and the association with ESCC prognosis

Replication Study in Chinese Population and Meta-Analysis Supports Association of the 11q23 Locus with Colorectal Cancer

<div><h3>Background</h3><p>A common single nucleotide polymorphism (SNP), rs3802842, located at 11q23, was identified by genome-wide association studies (GWAS) to be significantly associated with the risk of colorectal cancer (CRC); however, the results of following replication studies were not always concordant. Thus, a case-control study and a meta-analysis were performed to clearly discern the effect of this variant in CRC.</p> <h3>Method and Findings</h3><p>We determined the genotypes of rs3802842 in 641 unrelated Chinese patients with CRC and 1037 cancer-free controls. Additionally, a meta-analysis comprising current and previously published studies was conducted. In our case-control study, significant associations between the polymorphism and CRC risk were observed in all genetic models, with an additive OR being 1.45 (95% CI = 1.26–1.67). The meta-analysis of 38534 cases and 39446 controls further confirmed the significant associations in all genetic models but with obvious between-study heterogeneity. Nevertheless, ethnicity, study type and whether subjects affected by Lynch syndrome could synthetically accounted for the heterogeneity. Besides, the cumulative and sensitivity analyses indicated the robust stability of the results.</p> <h3>Conclusion</h3><p>The results from our case-control study and meta-analysis provided convincing evidence that rs3802842 significantly contributed to CRC risk.</p> </div

The characteristics of included studies.

<p>Abbreviations: GWAS, genome-wide association studies; SD, standard deviation; HRM, high resolution melt curve analysis.</p>a<p>The study included some Lynch syndrome patients.</p>b<p>The study only provided an adjusted additive OR.</p>c<p>The study only provided an allelic OR.</p>d<p>The percentage of patients having a family history of cancer.</p

Association between rs3802842 and colorectal cancer risk in a Chinese population^a.

<p>Abbreviations: OR, Odds ratio; 95% CI, 95% confidence interval.</p>a<p>ORs and their corresponding 95% CIs were calculated by multivariate logistic regression model after adjusting for age and sex.</p>b<p>The association between rs3802842 and colorectal cancer risk turned to be null significant after Bonferroni correction for multiple testing was applied.</p

Meta-analysis of the rs3802842 in association with colorectal cancer risk^a.

a<p>Crude ORs were combined in a fixed- or random- effects model.</p>b<p>Both crude and adjusted ORs were combined.</p>c<p>The association between rs3802842 and colorectal cancer risk turned to be null significant after Bonferroni correction for multiple testing was applied.</p

The characteristics of the study population.

a<p>Age was represented as mean±standard deviation.</p>b<p><i>P</i> value was calculated by the <i>x</i>² test.</p>c<p><i>P</i> value was calculated by the <i>t</i> test.</p

Supplemental Material, Table_S2_PH-assumption_tests_of_different_variables - High TSTA3 Expression as a Candidate Biomarker for Poor Prognosis of Patients With ESCC

<p>Supplemental Material, Table_S2_PH-assumption_tests_of_different_variables for High TSTA3 Expression as a Candidate Biomarker for Poor Prognosis of Patients With ESCC by Jie Yang, Pengzhou Kong, Jian Yang, Zhiwu Jia, Xiaoling Hu, Zianyi Wang, Heyang Cui, Yanghui Bi, Yu Qian, Hongyi Li, Fang Wang, Bin Yang, Ting Yan, Yanchun Ma, Ling Zhang, Caixia Cheng, Bin Song, Yaoping Li, Enwei Xu, Haiyan Liu, Wei Gao, Juan Wang, Yiqian Liu, Yuanfang Zhai, Lu Chang, Yi Wang, Yingchun Zhang, Ruyi Shi, Jing Liu, Qi Wang, Xiaolong Cheng, and Yongping Cui in Technology in Cancer Research & Treatment</p

Supplemental Material, Table_S1_Information_of_104_ESCC_patients - High TSTA3 Expression as a Candidate Biomarker for Poor Prognosis of Patients With ESCC

<p>Supplemental Material, Table_S1_Information_of_104_ESCC_patients for High TSTA3 Expression as a Candidate Biomarker for Poor Prognosis of Patients With ESCC by Jie Yang, Pengzhou Kong, Jian Yang, Zhiwu Jia, Xiaoling Hu, Zianyi Wang, Heyang Cui, Yanghui Bi, Yu Qian, Hongyi Li, Fang Wang, Bin Yang, Ting Yan, Yanchun Ma, Ling Zhang, Caixia Cheng, Bin Song, Yaoping Li, Enwei Xu, Haiyan Liu, Wei Gao, Juan Wang, Yiqian Liu, Yuanfang Zhai, Lu Chang, Yi Wang, Yingchun Zhang, Ruyi Shi, Jing Liu, Qi Wang, Xiaolong Cheng, and Yongping Cui in Technology in Cancer Research & Treatment</p