Preparing Single-cell DNA Library Using Nextera for Detection of CNV

Liu, Xi; Leong, Patrick P.; Mihajlović, Aleksandar

doi:10.21769/bioprotoc.3175

Cited by 2 publications

(2 citation statements)

References 13 publications

(3 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…No. MS-102-3001) for sequencing 80 bases for Read1 and 70 bases for Read2, after quantitation following the manufacturer’s protocol 14 .…”

Section: Methodsmentioning

confidence: 99%

“…As a result, the precision can range from 0 to 90% in the worst cases using simulated data 12 . Previously, we published a novel single-cell DNA sequencing scheme 13 , 14 , dubbed Barcodes_in_Genome_sequencing (BIGseq), which has the potential to detect the integer copy numbers at single base resolution. In order to reach that potential, the coverage of every haploid molecule in the single cell library needs to be high enough and a secondary analysis algorithm can process the library data properly.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Reconstructing and counting genomic fragments through tagmentation-based haploid phasing

Leong¹,

Mihajlović

Bogdanović

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

Single-cell sequencing provides a new level of granularity in studying the heterogeneous nature of cancer cells. For some cancers, this heterogeneity is the result of copy number changes of genes within the cellular genomes. The ability to accurately determine such copy number changes is critical in tracing and understanding tumorigenesis. Current single-cell genome sequencing methodologies infer copy numbers based on statistical approaches followed by rounding decimal numbers to integer values. Such methodologies are sample dependent, have varying calling sensitivities which heavily depend on the sample’s ploidy and are sensitive to noise in sequencing data. In this paper we have demonstrated the concept of integer-counting by using a novel bioinformatic algorithm built on our library construction chemistry in order to detect the discrete nature of the genome.

show abstract

“…No. MS-102-3001) for sequencing 80 bases for Read1 and 70 bases for Read2, after quantitation following the manufacturer’s protocol 14 .…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Reconstructing and counting genomic fragments through tagmentation-based haploid phasing

Leong¹,

Mihajlović

Bogdanović

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics

Kim,

Yeom

et al. 2023

Nat Commun

View full text Add to dashboard Cite

Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities. By incorporating cell barcodes during MDA, bMDA streamlines library preparation in one pot, thereby overcoming a key bottleneck in spatial genomics. We apply bMDA to the integrative spatial analysis of triple-negative breast cancer tissues by examining copy number alterations, single nucleotide variations, structural variations, and kataegis signatures for each spatial microniche. This enables the assessment of subclonal evolutionary relationships within a spatial context. Therefore, bMDA has emerged as a scalable technology with the potential to advance the field of spatial genomics significantly.

show abstract

Preparing Single-cell DNA Library Using Nextera for Detection of CNV

Cited by 2 publications

References 13 publications

Reconstructing and counting genomic fragments through tagmentation-based haploid phasing

Reconstructing and counting genomic fragments through tagmentation-based haploid phasing

Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics

Contact Info

Product

Resources

About