Dataset Information

Precise diagnosis of three top cancers using dbGaP data.

ABSTRACT: The challenge of decoding information about complex diseases hidden in huge number of single nucleotide polymorphism (SNP) genotypes is undertaken based on five dbGaP studies. Current genome-wide association studies have successfully identified many high-risk SNPs associated with diseases, but precise diagnostic models for complex diseases by these or more other SNP genotypes are still unavailable in the literature. We report that lung cancer, breast cancer and prostate cancer as the first three top cancers worldwide can be predicted precisely via 240-370 SNPs with accuracy up to 99% according to leave-one-out and 10-fold cross-validation. Our findings (1) confirm an early guess of Dr. Mitchell H. Gail that about 300 SNPs are needed to improve risk forecasts for breast cancer, (2) reveal an incredible fact that SNP genotypes may contain almost all information that one wants to know, and (3) show a hopeful possibility that complex diseases can be precisely diagnosed by means of SNP genotypes without using phenotypical features. In short words, information hidden in SNP genotypes can be extracted in efficient ways to make precise diagnoses for complex diseases.

SUBMITTER: Liu XQ

PROVIDER: S-EPMC7804208 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Precise diagnosis of three top cancers using dbGaP data.

Liu Xu-Qing XQ Liu Xin-Sheng XS Rong Jian-Ying JY Gao Feng F Wu Yan-Dong YD Deng Chun-Hua CH Jiang Hong-Yan HY Li Xiao-Feng XF Chen Ye-Qin YQ Zhao Zhi-Guo ZG Liu Yu-Ting YT Chen Hai-Wen HW Li Jun-Liang JL Huang Yu Y Ji Cheng-Yao CY Liu Wen-Wen WW Luo Xiao-Hu XH Xiao Li-Li LL

Scientific reports 20210112 1

The challenge of decoding information about complex diseases hidden in huge number of single nucleotide polymorphism (SNP) genotypes is undertaken based on five dbGaP studies. Current genome-wide association studies have successfully identified many high-risk SNPs associated with diseases, but precise diagnostic models for complex diseases by these or more other SNP genotypes are still unavailable in the literature. We report that lung cancer, breast cancer and prostate cancer as the first three ...[more]

PMID: 33436913

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Project description:ObjectivesTo evaluate the performance of a novel three-dimensional (3D) joint convolutional and recurrent neural network (CNN-RNN) for the detection of intracranial hemorrhage (ICH) and its five subtypes (cerebral parenchymal, intraventricular, subdural, epidural, and subarachnoid) in non-contrast head CT.MethodsA total of 2836 subjects (ICH/normal, 1836/1000) from three institutions were included in this ethically approved retrospective study, with a total of 76,621 slices from non-contrast head CT scans. ICH and its five subtypes were annotated by three independent experienced radiologists, with majority voting as reference standard for both the subject level and the slice level. Ninety percent of data was used for training and validation, and the rest 10% for final evaluation. A joint CNN-RNN classification framework was proposed, with the flexibility to train when subject-level or slice-level labels are available. The predictions were compared with the interpretations from three junior radiology trainees and an additional senior radiologist.ResultsIt took our algorithm less than 30 s on average to process a 3D CT scan. For the two-type classification task (predicting bleeding or not), our algorithm achieved excellent values (≥ 0.98) across all reporting metrics on the subject level. For the five-type classification task (predicting five subtypes), our algorithm achieved > 0.8 AUC across all subtypes. The performance of our algorithm was generally superior to the average performance of the junior radiology trainees for both two-type and five-type classification tasks.ConclusionsThe proposed method was able to accurately detect ICH and its subtypes with fast speed, suggesting its potential for assisting radiologists and physicians in their clinical diagnosis workflow.Key points• A 3D joint CNN-RNN deep learning framework was developed for ICH detection and subtype classification, which has the flexibility to train with either subject-level labels or slice-level labels. • This deep learning framework is fast and accurate at detecting ICH and its subtypes. • The performance of the automated algorithm was superior to the average performance of three junior radiology trainees in this work, suggesting its potential to reduce initial misinterpretations.

Dataset Information

Precise diagnosis of three top cancers using dbGaP data.

Publications

Precise diagnosis of three top cancers using dbGaP data.

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