Genomewide SNP marker identification associated with drought tolerance in oil palm

Yono D, Nugroho YA, Tanjung ZA, Utomo C, Liwang T. 2021. Genomewide SNP marker identification associated with drought tolerance in oil palm. Biodiversitas 22: 3138-3144. Drought stress is one of the abiotic stresses that frequently occurred in the oil palm plantation and has a negative impact on fresh fruit bunch (FFB) production. Therefore, drought-tolerant palms are essential to be selected to mitigate this challenge. In Indonesia, several oil palm plantation areas have a dry climate, such as Lampung province. Distinct yield performance palms were identified from well-recorded agronomic trials in these areas, where the palms are frequently exposed to drought stresses every year and lead them to suffer from water deficit response. Group of high and low-yielding palms was selected based on FFB production of each palm for at least ten constitutive years. The double digest restriction amplified DNA (ddRAD) genotyping methods were used to capture the Single Nucleotide Polymorph (SNP) variant from pools of sample association datasets. At least, 538k SNPs were identified from these pooled datasets. A bulked segregant analysis with a Case-Control approach was implemented to screen the contrast SNP profiles between both pools. A total of 56 association signals was selected from sequential filtering. These SNP sites are located in 21 genes. Further SNP validation and phenotypic verification are necessary to obtain SNPs marker for drought-tolerant palm selections.

Multispectral Imaging for Metallic Biopsy Marker Detection During MRI-Guided Breast Biopsy: A Feasibility Study for Clinical Translation

PurposeTo assess the feasibility and diagnostic accuracy of multispectral MRI (MSI) in the detection and localization of biopsy markers during MRI-guided breast biopsy.MethodsThis prospective study included 20 patients undergoing MR-guided breast biopsy. In 10 patients (Group 1), MSI was acquired following tissue sampling and biopsy marker deployment. In the other 10 patients (Group 2), MSI was acquired following tissue sampling but before biopsy marker deployment (to simulate deployment failure). All patients received post-procedure mammograms. Group 1 and Group 2 designations, in combination with the post-procedure mammogram, served as the reference standard. The diagnostic performance of MSI for biopsy marker identification was independently evaluated by two readers using two-spectral-bin MR and one-spectral-bin MR. The κ statistic was used to assess inter-rater agreement for biopsy marker identification.ResultsThe sensitivity, specificity, and accuracy of biopsy marker detection for readers 1 and 2 using 2-bin MSI were 90.0% (9/10) and 90.0% (9/10), 100.0% (10/10) and 100.0% (10/10), 95.0% (19/20) and 95.0% (19/20); and using 1-bin MSI were 70.0% (7/10) and 80.0% (8/10), 100.0% (8/8) and 100.0% (10/10), 85.0% (17/20) and 90.0% (18/20). Positive predictive value was 100% for both readers for all numbers of bins. Inter-rater agreement was excellent: κ was 1.0 for 2-bin MSI and 0.81 for 1-bin MSI.ConclusionMSI is a feasible, diagnostically accurate technique for identifying metallic biopsy markers during MRI-guided breast biopsy and may eliminate the need for a post-procedure mammogram.

The clinical significance of CTC enrichment by GPC3-IML and its genetic analysis in hepatocellular carcinoma

Background This research was to develop a special method for enriching Circulating tumor cells (CTCs) of Hepatocellular carcinoma (HCC) by Glypican-3 immunoliposomes (GPC3-IML), and to analyze the correlation between the CTCs count and tumor malignancy, as well as to investigate the mutation characteristics of CTC-derived NGS. Results In this study characterization of physical parameters was performed with the preparation of GPC3-IML. CTCs in peripheral blood of HCC patients were further separated and identified. Immunofluorescence was used to identify CTCs for further counting. By this means, the correlation between CTCs count and clinicopathological features was analyzed, and the genetic mutation characteristics of NGS derived from CTCs were investigated and compared with that of tissue NGS. Results showed that compared with EpCAM and vimentin, GPC-3 had a stronger CTCs separation ability. There was a correlation between "positive" count of CTCs (≥ 5 PV-CTC per 7.5 ml blood) and BCLC stage (P = 0.055). The result of CTC-NGS was consistent with that of tissue-NGS in 60% cases, revealing that KMT2C was a common highly-frequent mutated gene. Conclusion The combination of immunomagnetic separation of CTCs and anti-tumor marker identification technology can be regarded as a new technology of CTCs detection in peripheral blood of patients with HCC. Trial registration EHBHKY2020-k-024. Registered 17 August 2020—Retrospectively registered