Table 5 Current methods available for single-cell genomic sequencing

DOP-PCR

DOP-PCR is a polymerase chain reaction (PCR) method that uses specific oligonucleotide primers and DNA polymerase to amplify specific DNA sequences; high amplification efficiency; applicable to DNA samples from a variety of sources, including genomic DNA and cDNA; may be over-amplified or selectively amplified; may cause non-specific amplification; restrictive selection

[130]

MDA

MDA is a technique for whole-genome amplification in low-complexity DNA samples; has whole-genome amplification, allele retention, and no need for specific primers; has limitations of amplification bias, localized error rates, and sample contamination; and costs low

[131]

LIANTI

LIANTI is an improved single-cell whole-genome amplification (WGA) method that accurately detects copy-number variations (CNVs) at a microscale resolution; It enables the observation of DNA replication origin firing patterns and addresses the origin of cytosine-to-thymine mutations in single-cell genomics; advancements in CNV detection, amplification fidelity, and the study of DNA replication and mutation profiles in single cells

[132]

META-CS

META-CS is a single-cell whole-genome amplification method that utilizes the complementarity of double-stranded DNA to accurately identify single-nucleotide variations (SNVs); the ability to amplify diploid and haploid cells, high success rate of single-cell amplification, simplified experimental procedure, and reduced sequencing cost; false positive mutations and inconsistent amplification efficiency

[133]

MALBAC

MALBAC is a single-cell whole genome amplification technique for amplifying DNA from a single cell; reduced amplification randomness and bias, increased homogeneity of amplification products; low error rate; limitations of reduced amplification quality, loss of complexity, and amplification bias

[134]

eWGA

eWGA is an enhanced whole-genome amplification technique used to amplify DNA samples starting from very low quantities to obtain sufficient amounts of DNA for subsequent analysis; characterized by high amplification efficiency, low amplification bias, homogeneity, and accuracy; limitations of preferential amplification, localized error rates, and co-amplification contamination; and relative economy

[135]

SISTOR

SISSOR is a method used for precise sequencing of single-cell genomes and haplotype analysis; based on a microfluidic processor to separate and amplify the DNA strands in individual cells; This enables independent sequencing of complementary strands and assembly of long haplotypes; low error rates and can generate DNA fragments that can be assembled into haplotype contigs

[136]

ScWGS

scWGS is a method that enables deep sequencing of the genomic DNA of individual cells; based on microfluidic technology and DNA amplification techniques; relatively lower throughput; capture mutations present in different cells, study rare events, not require a large amount of starting material; amplification bias, complex data analysis; cost high

[137]

scWES

scWESis a targeted sequencing method that allows for the sequencing of the exome, including the coding regions of the genome, within individual cells; provides a comprehensive view of the genetic variations present in the coding regions of single cells, including single nucleotide variants (SNVs), small insertions or deletions (indels), and structural variations; relatively lower throughput; amplification biases and technical noise; relatively expensive; studying cellular heterogeneity

[138]

scDNA-seq

scDNA-seq allows for the whole-genome sequencing of individual cells, providing a comprehensive view of genomic variations, including mutations, copy number variations, and structural variations; relatively low throughput; detecting low-frequency mutations and copy number variations; Limitations include sequencing depth constraints, potential amplification biases, and technical noise; relatively expensive; data complex; reveals information about genetic heterogeneity between cells and cell evolution

[139]