№ files_lp_3_process_9_38208
File format: docx
Character count: 15808
File size: 56 KB
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
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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
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
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
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
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
Note:
Year
Year:
2023
Region / City:
Australia
Theme:
Paediatric Oncology, Pharmacology
Document Type:
Medical Submission
Organization / Institution:
Novartis Pharmaceuticals Australia Pty Limited
Author:
Novartis Pharmaceuticals Australia Pty Limited
Target Audience:
Medical practitioners, oncologists, pharmacists, healthcare providers
Period of Validity:
Not specified
Approval Date:
6 December 2023
Date of Amendments:
Not specified
Year:
2021
Region / city:
Australia
Topic:
Oncology / Pharmaceutical
Document Type:
Submission
Agency:
Pharmaceutical Benefits Advisory Committee (PBAC)
Author:
AstraZeneca Pty Ltd
Target Audience:
Medical professionals, regulatory authorities
Validity Period:
2021-2026
Approval Date:
20 April 2021
Modification Date:
Not specified
Year:
2023
Region / city:
Kawasaki, Tokyo, Hamamatsu, Japan
Subject:
Biomedical research, gene editing, transgenic mice
Document type:
Research appendix
Organization / institution:
In-Vivo Science Inc., CLEA Japan, Japan SLC Inc., Thermo Fisher Scientific
Author:
Not specified
Target audience:
Researchers, scientists in the field of molecular biology and genetics
Effective period:
Not specified
Approval date:
Not specified
Modification date:
Not specified
Year:
N/A
Region / City:
N/A
Theme:
Mutation Frequency, Bacterial Genetics
Document Type:
Research Data
Author:
N/A
Target Audience:
Researchers in Genetics, Microbiology
Period of Action:
N/A
Date of Approval:
N/A
Date of Modifications:
N/A
Note:
Year
Topic:
Genetics, Inheritance
Document Type:
Student Activity Sheet
Target Audience:
Students
Authors:
Mengru Wang; Ying Bai; Dan Jiang; Yue Wang; Yingchao Zhou; Mengchen Zhou; Yilin Chen; Chenguang Yu; Xiangyi Wang; Qiang Guo; Lingfeng Zha; Qianqian Li; Zhubing Cao; Jianfei Wu; Shumei Shi; Qing Wang; Chengqi Xu; Xiangdong Kong; Xin Tu
Affiliations:
Key Laboratory of Molecular Biophysics of the Ministry of Education, Center for Human Genome Research, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Genetic and Prenatal Diagnosis Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Qingdao Women and Children’s Hospital, Qingdao University, Qingdao, China; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
Correspondence:
Xin Tu ([email protected]
Note:
)
Country:
China
Study Type:
Clinical and molecular genetic research study
Subject:
12-year-old male patient of Chinese ancestry
Genetic Focus:
HOIP (RNF31) frameshift mutation c.1882delG
Comparison Cases:
HOIP-1; HOIP-2
Pathway Analyzed:
NF-kappaB signaling pathway; TNF-induced cell death
Clinical Features:
Recurrent infections; necrotizing lymphadenitis; Epstein-Barr virus infection; lobar pneumonia; splenomegaly; immunoglobulin subclass deficiency
Laboratory Analyses:
Immunological evaluation; viral testing; lymph node biopsy; bone marrow aspiration; gene panel analysis
Treatment:
Intravenous immunoglobulin; antibiotics; anti-inflammatory therapy
Supplementary Materials:
Table S1 (List of analyzed genes); Table S2 (Summary of clinical phenotype of patients with HOIP mutations); Figure S1 (LUBAC binding assay)
Author:
Shuchismita Dutta
Institution:
Institute of Quantitative Biomedicine, Rutgers University, Piscataway NJ 08854
Geographic location:
Toms River, New Jersey, United States
Year of case:
2008
Year of publication:
2011
Journal referenced:
New England Journal of Medicine
Related article:
Patch (Toms River edition)
Medical focus:
Cyanosis in a newborn
Genetic focus:
Hemoglobin Toms River mutation (V67M in γ-globin)
Protein studied:
Fetal hemoglobin (α2γ2)
Research methods referenced:
DNA sequencing, structural analysis using Protein Data Bank, laser photolysis, rapid mixing kinetics
Protein database referenced:
Protein Data Bank
Structure visualization tool referenced:
iCn3D
Native protein structure referenced:
PDB ID 4MQJ
Biological system used:
Escherichia coli expression system
Type of document:
Educational case study with research analysis questions
Intended audience:
Students in biochemistry, molecular biology, or biomedical sciences
Subject area:
Molecular basis of cyanosis and hemoglobin mutation
Year:
Not specified
Region / City:
Not specified
Theme:
Genetics, Oncology
Document Type:
Research Article
Organization / Institution:
Not specified
Author:
Not specified
Target Audience:
Researchers, Scientists, Medical Professionals
Period of Validity:
Not specified
Approval Date:
Not specified
Date of Changes:
Not specified
Document Type:
Supplementary appendix
Subject Area:
Oncology
Disease Focus:
Renal cell carcinoma
Content Type:
Tables and figures
Population:
Patients with renal cell carcinoma
Sample Size:
43 patients (baseline characteristics), 19 patients (tumor mutation burden), 8 patients (PD-L1 expression)
Variables:
Age, sex, ECOG performance status, histology, sarcomatoid/rhabdoid differentiation, IMDC risk group, metastases, prior nephrectomy, therapy line
Biomarkers:
Tumor mutation burden, PD-L1 expression
Outcomes:
Best overall response, overall survival
Response Categories:
Partial response, stable disease, progressive disease
Institutions Referenced:
Eastern Cooperative Oncology Group, International Metastatic RCC Database Consortium
Language:
English
Data Presentation:
Quantitative tabular data with percentages and counts
Year:
2026
Region/Location:
Not specified
Subject:
Melanoma research
Document type:
Supplementary data tables
Institution:
Research laboratory / academic study
Author:
Not specified
Sample size:
NEVI (14), Primary Malignant Melanoma (23), Metastatic Melanoma (15)
Methods:
Immunohistochemistry for PD-L1, BRAF codon 600 genotyping, inflammatory scoring
Cell lines:
Human melanoma cultured cells
Treatment:
IFN-gamma induction
Data metrics:
%PD-L1 expression, inflammation score, ∆MFI for PD-L1 and MHC I
Context:
Archival melanoma tissue samples and cultured melanoma cell lines analyzed for PD-L1 expression, BRAF mutation status, and immune response markers in experimental study
Year:
N/A
Region / city:
N/A
Topic:
Cancer research, survival analysis
Document type:
Supplementary material
Author:
N/A
Target audience:
Researchers, medical professionals
Period of validity:
N/A
Approval date:
N/A
Date of changes:
N/A
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
Year:
2025
Location:
Jerusalem, Palestine
Topic:
Ophthalmology, Genetic Retinal Disorders
Document Type:
Case Report
Institution:
St. John of Jerusalem Eye Hospital Group
Authors:
Salam Iriqat, Rawan Ayyad, Yahya Alswaiti
Target Audience:
Ophthalmologists, Geneticists
Patient Age:
25
Patient Sex:
Female
Genetic Finding:
Homozygous nonsense mutation in CDHR1 c.1632C>A, p.(Tyr544*)
Clinical Features:
Progressive nyctalopia, peripheral vision loss, macular atrophy, pale optic discs, color vision deficiency
Pregnancy Status:
First trimester onset of symptoms, deterioration continued postpartum
Diagnostic Methods:
Fundus examination, Optical Coherence Tomography, Full-field Electroretinography, Genetic Testing
Consanguinity:
Parents are first cousins
Ethics:
Written informed consent obtained
Funding:
None
Conflicts of Interest:
None reported
References:
Included in the text
Year:
2026
Region / City:
Pretoria, South Africa; Chennai and Bangalore, India
Subject:
Carcinogenesis modeling
Document type:
Research article
Institution:
University of Pretoria; Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology; HKBK College of Engineering
Authors:
V. S. S. Yadavalli, S. Udayabaskaran, C. T. Dora Pravina, S. Sree Lakshmi
Corresponding author:
[email protected]
Methodology:
Two-stage stochastic modeling in a random environment
Keywords:
Age-dependent two-stage stochastic model, Normal cell, Intermediate cell, Malignant cell, Random environment