Genome Sizes of Bacterial Species Detected in Cell-Free DNA of Patients with Acute Leukemia and Sepsis, Including Those Undergoing Bone Marrow Transplantation
Authors/Creators
-
Mathur, Arpit
(Data curator)1
- Anam, Karishma (Data curator)1
- Gawde, Vaibhav (Annotator)1
- Terse, Vishram (Editor)1
- Bhanshe, Prasanna (Research group)1
- Joshi, Swapnali (Research group)1
- Chaudhary, Shruti (Research group)1
- Chatterjee, Gaurav (Research group)1
- Rajpal, Sweta (Research group)1
- Tembhare, Prashant (Research group)1
- Mirgh, Sumeet (Research group)1
- Shetty, Alok (Research group)2
- Punatar, Sachin (Research group)1
- Nayak, Lingaraj (Research group)1
- Jain, Hasmukh (Research group)1
- Sengar, Manju (Research group)1
- Bagal, Bhausaheb (Research group)1
- Subramanian, PG (Research group)1
- Gujral, Sumeet (Research group)1, 2
- Jindal, Nishant (Research group)1
- Shetty, Dhanalaxmi (Research group)1
- Khattry, Navin (Research group)1
- Gokarn, Anant (Contact person)1
- Patkar, Nikhil (Supervisor)1
-
1.
Advanced Centre for Treatment, Research and Education in Cancer
-
2.
Tata Memorial Hospital
Description
Next Generation Sequencing (NGS) analysis of Cell Free DNA provides valuable insights into spectrum of pathogenic species (particularly bacterial) present in blood. Patients with Sepsis often face problem like delay of treatment regiment (combination or cocktail of antibiotics) due to long turn around time (TAT) of classical and standard blood culture procedure. NGS gives results with lower TAT along with high depth coverage. Use of NGS may therby be a possible solution to decide treatment regiment of patients without losing precious time and more accurately possibly saving lifes.
Our curated dataset is of bacterial species or strains detected along with their genome size in 107 AML patients diagnosed as having Sepsis clinically. Cell free DNA profiles of patients were build and sequencing was done in Illumina (NovaSeq and NextSeq). Bioinformatic analysis was peformed using kraken2 classification algorithm and reference bacterial index devloped by Carlo Ferravante et al (Zenodo 2020) (link: https://zenodo.org/records/4055180) was used.
Genome size annotation is important in metagenomics since for the use of depth of coverage (abundance), genome size is required. In metagenomic classification algorithms like kraken/kraken2 output computes reads assigned only and not abundance. To compute abundance, we build Genome size annotator tool (https://github.com/patkarlab/Genome-Size-Annotation) which provides genome size for each species detected given its taxid is available.
Files
AML Sepsis Patients Cell Free DNA Species.csv
Files
(191.7 kB)
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Additional details
Additional titles
- Alternative title (English)
- Dataset of Bacterial Species along with their genome size, detected in Cell Free DNA of Acute Leukemia Patients diagnosed with Sepsis including those undergone bone marrow transplant
Funding
- Lady Tata Memorial Trust
Software
- Repository URL
- https://github.com/patkarlab/Genome-Size-Annotation
- Programming language
- Unix Assembly
- Development Status
- Active