Case Interpretations.
Case 1 Genomic variation mapping reveals the origin of cultivated rice
Background
Cultivated rice is one of the most important crops and has been domesticated from wild rice for thousands of years. Cultivated rice is one of the most important developments in human history and has greatly contributed to the development of human civilization, but its origin and domestication process was controversial.
Study
In this study, the researchers used rice as the material, and carried out whole-genome sequencing of 446 wild rice species and 1083 cultivated japonica and indica rice species from different regions. The researchers constructed a relatively comprehensive map of the structural variation of the rice genome, revealing the domestication and origin process of cultivated japonica and indica rice, and provided important genetic resources for molecular breeding of rice, as well as important genomic approach for crop domestication research.
Figure 1. Domestication and origin of cultivated rice
Results
1. Based on whole genome sequencing, NJ tree and PCA analysis, 446 wild rice from different regions could be classified into three types: Or-I, Or-II and Or-III, and there was a strong correlation between the classification and geographical distribution;
2. resequencing analysis of 1083 cultivated japonica rice and indica rice revealed that cultivated japonica rice and indica rice originated from Or-I and Or-III, respectively;
3. the domestication of japonica rice originated earlier than indica rice.
Case 2 Ultra-low depth whole genome sequencing based on cfDNA to differentiate benign and malignant neurofibroma lesions
Background
Neurofibromatosis type 1 (NF1) is a common hereditary syndrome of cancer susceptibility. Malignant peripheral nerve sheath tumour (MPNST), an aggressive soft tissue sarcoma caused by a benign plexiform neurofibroma (PN) precursor lesion, is the leading cause of death in patients with NF1. Accurate diagnosis of the transition from PN to MPNST is challenging, as cross-sectional imaging findings of the two are difficult to differentiate, and intra-lesional heterogeneity may lead to false-negative biopsy results, often causing delayed diagnosis of MPNST and even worsening prognosis.
Study
The team prospectively collected blood samples from 23 patients with PN, 14 patients with MPNST who had not yet received treatment and 16 healthy individuals. The cfDNA was isolated from the blood samples and analysed using ULP-WGS for cfDNA detection. The aim was to differentiate MPNST from benign PN in a non-invasive manner by analysing and quantifying genomic copy number variants (CNA) in plasma cfDNA.
Figure 1. Overview of the study
Results
ULP-WGS is a highly sensitive and quick and simple method to non-invasively differentiate patients with MPNST from benign precursors, providing the first evidence of the ability of liquid biopsy to differentiate benign from malignant tumours in hereditary cancer susceptibility syndromes. This liquid biopsy technique can determine ambiguous imaging findings and has the potential to monitor PN patients as a biomarker test for MRD and treatment response, facilitating early detection of MPNST and laying the foundation for improved early cancer detection and surveillance in high-risk cancer susceptible populations.
reference：
1. Huang X, Kurata N, Wei X, et al. A map of rice genome variation reveals the origin of cultivated rice[J]. Nature, 2012, 490(7421):497-501.
2. Li, S., Noor, Z.S., Zeng, W. et al. Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis. Nat Commun 12, 4172(2021)
3. Peneder, P., Stütz, A.M., Surdez, D. et al. Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. Nat Commun 12, 3230(2021)
