№ files_lp_4_process_1_39507
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Supplementary research article detailing sequencing depth, DNJ-stem definitions, and clonal evolution mechanisms in KMT2A-rearranged and germline leukemia patient samples.
Year: 2026
Region / City: Not specified
Topic: Immunogenetics, Clonal evolution in leukemia
Document type: Supplementary materials and methods
Institution: Research laboratory, unspecified
Author: Not specified
Target audience: Researchers in hematology and molecular biology
Period of study: Patient cohort sampling period not specified
Date of approval: Not specified
Sequencing depth: IGH-DJ library average 104,771 reads per KMT2A-rearranged sample, IGH-VJ library average 42,640 reads per KMT2A-rearranged sample
Patient cohort: KMT2A-rearranged (n=18), KMT2A-germline (n=137)
Clonal evolution assessment: DNJ-stem analysis with VH-DJH and VH-rep mechanisms
Sample materials: Bone marrow, peripheral blood, bone marrow trephine
Immunophenotype: pro-B, c-/pre-B
Age at entry: 18–56 years
White blood cell count: specified per patient
Gene fusion: KMT2A-MLLT1, KMT2A-AFF1, KMT2A-UBASH3B
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Defining breeding objectives for self-pollinated, cross-pollinated, and clonal crops
Note: Year
Topic: Plant Breeding, Crop Improvement
Document Type: Educational Material
Target Audience: Students in crop improvement, plant breeding
Contextual Description: A training document for crop improvement students, focusing on defining breeding objectives for different crop types.
USDA National Clonal Germplasm Repository for Citrus and Dates, Annual Report to the Citrus Crop Germplasm Committee and Date Crop Germplasm Committee, CY 2017
Year: 2017
Region / City: Riverside, CA
Subject: Citrus and Date Germplasm
Document Type: Annual Report
Organization: USDA
Author: MaryLou Polek, Robert Krueger, Manjunath Keremane, Vicki Newman, Brittany Moreland, Esteban Rodriguez, Patricia Moore, Lee Gross, Amanda Rawstern, Brooke Gómez, Benedict Mamaril, Andres Márquez, Chidera Mbonu, Ngoc Tran, Gerardo Uribe
Target Audience: Researchers, Agricultural Professionals
Period of Validity: CY 2017
Date Approved: 2017
Date of Modifications: N/A
Description: Annual report detailing activities, acquisitions, and research efforts related to citrus and date palm germplasm preservation and cryopreservation at the USDA National Clonal Germplasm Repository.
Integrative dual ctDNA 5mC/5hmC methylomics and clonal reconstruction in metastatic prostate cancer
Year: 2026
Region / City: Not specified
Topic: Cancer genomics, epigenetics, prostate cancer
Document type: Supplementary material
Institution: Not specified
Authors: Chennan Li et al.
Target audience: Researchers in oncology and molecular biology
Sample type: Plasma and buffy coat
Methods: ctDNA sequencing, 5mC/5hmC methylomics, clonal reconstruction
Timepoints: Baseline, restaging, progression, off-study
Genes analyzed: AR, BRCA2, erythroid markers, platelet/megakaryocyte markers, globins
Data included: Sequencing metrics, methylation percentages, gene-level events, survival analysis
Associated figures: 8 supplementary figures, 2 supplementary tables
Statistical analyses: Spearman correlation, Kruskal-Wallis test, Mann-Whitney U test, Kaplan-Meier survival estimates, log-rank test
Supplementary MethodsAssembly of Working Group on Breast Cancer Germline Testing
Year: 2024
Region / City: International
Subject: Breast Cancer, Genetic Testing
Document Type: Expert Consensus Report
Organization / Institution: ESMO Precision Oncology Working Group
Author: ESMO Precision Oncology Working Group
Target Audience: Clinicians, Medical Oncologists, Geneticists
Period of validity: 2024
Approval Date: Not specified
Date of Changes: Not specified
Supplementary file 1a – Study design and methodology of the studies on pedigree-based germline mutation rate estimation
Year: 2016-2021
Species studied: Human, Collared flycatcher, Herring, Cattle, Chimpanzee, Mouse, Rhesus macaque, Grey mouse lemur, Cat, Marmoset
Number of trios: 13, 7, 12, 5, 1550, 150, 8, 19, 2, 11, 1
Sequencing machine: Illumina HiSeq, Illumina HiSeq 2500, Illumina HiSeq X, Illumina HiSeq 2000, Illumina HiSeq 2000, Complete Genomics Inc.
Sequencing depth: 24.7X, 40X, 60X, 65.8X, 23X, 78X, 28.5X, 81X, 34.5X, 41X, 75X
Mapping: BWA, BWA mem, GATK, Picard MarkDuplicates
Variant calling method: DeNovoGear, GATK, FreeBayes, Strelka
FDR: 83.1%, 35%, 13%, 5.9%, 3%, 88%, 57.4%, 91.5%, 91%, 44%
FNR: 20%, 80%, 32%, 44%, 45%
Method: Poisson distribution, Customized filtering, Manual curation
Software: GATK 3.3.0, GATK 3.5, Samtools
Validation method: Sanger sequencing, Manual curation, Simulation
Date of approval: 2016-2021
End of study: 2021
Supplementary Table 1. Rare germline pathogenic, likely pathogenic, or deleterious (P/LP/D) variants (n=51) in BRCA2, ATM, NBN, and PALB2 identified among men of African ancestry.
Note: Gene
Year: 2020
Region / city: Not specified
Topic: Genetic variants, Germline mutations
Document type: Supplementary Table
Author: Matejcic et al
Target audience: Researchers in genetics, oncology
Period of validity: Not specified
Approval date: Not specified
Modification date: Not specified
FAST FACTS A211801 – BRCA-P Phase 3 Randomized Double-Blind Placebo-Controlled Study of Denosumab for Prevention of Breast Cancer in Women with BRCA1 Germline Mutation
Study ID: A211801
Study name: BRCA-P
Document type: Clinical trial eligibility criteria summary
Study type: Randomized, double-blind, placebo-controlled clinical trial
Phase: Phase 3
Geographic scope: International multi-center study
Medical field: Oncology
Target condition: Breast cancer prevention in BRCA1 germline mutation carriers
Investigational drug: Denosumab
Control: Placebo
Population: Women with confirmed deleterious or likely deleterious BRCA1 germline mutation aged 25–55 years
Key inclusion criteria: No evidence of breast cancer by MRI or mammography and clinical breast examination within 6 months, no clinical evidence of ovarian cancer, ECOG performance status 0–1, written informed consent
Key exclusion criteria: Prior bilateral mastectomy, history of breast or ovarian cancer, prior denosumab use, pregnancy or lactation, clinically relevant hypocalcaemia, certain prior hormonal or investigational treatments, significant medical or psychiatric conditions, active hepatitis B, hepatitis C, or HIV infection
CRISPR/Cas9 gene editing in the human germline: current progress and challenges
Year: 2020
Region / City: Ghent, Belgium
Topic: Human germline gene editing
Document type: Review article
Institution: Ghent University Hospital, Center for Medical Genetics Ghent
Authors: Bekaert B., Boel A., Cosemans G., De Witte L., Menten B., Heindryckx B.
Corresponding author: [email protected]
Keywords: human germline gene editing, loss-of-heterozygosity, mosaicism, CRISPR/Cas9
Focus: Preimplantation embryos and oocytes
Methodologies: Knock-out and knock-in experiments, base editing, prime editing
Challenges addressed: Mosaicism, off-target editing, loss-of-heterozygosity
Ethical considerations: Use of non-viable embryos, evaluation of ethical implications of HGGE
Publication type: Peer-reviewed scientific review
Topics: KMT2A-rearranged clonal Germline