Table 2.

Methods to analyze mosaicism in the brain.

		Technique	Pros	Cons	References
Single cell amplification	MDA	phi29 polymerase uses strand displacement to achieve highly processive amplification of genomic DNA in an isothermal reaction	Low error rate for SNVs; coverage of most of the genome in long (10–50kb) amplicons	High copy-number noise at megabase scale	(8–14)
	DOP-PCR	Fragmentation of DNA followed by ligation of universal adapters and PCR	Even copy-number profile at small scale	High SNV error rate; small amplicon size	(13,15–17)
	Hybrid PCR/ isothermal	Quasilinear preamplification using random primers followed by PCR amplification	Even copy-number profile at small scale	High SNV error rate; Short (0.5-1.5kb) amplicons.	(18–20)
	Clonal expansion/somatic cell nuclear transfer (SCNT)	Cellular DNA replication is used to amplify the genome of a single cell of interest. Proliferative cells can be grown clonally in culture. For terminal differentiated cells, the nucleus can be reprogrammed using SCNT.	Cellular replication machinery operates at much higher fidelity than chemical methods.	Clonal growth in culture is limited to proliferative cells. SCNT has very low efficiency and is not amenable to human cells for technical and ethical reasons.	(21,22)
Trio sequencing		Standard whole-genome sequencing with family information to identify germline de novo and somatic mutations in probands	Avoids whole-genome amplification	Lack of single-cell resolution; low-fraction mosaics hard to distinguish from errors	(23–25)
Enrichment	Transposon insertion mapping	PCR-based techniques that target degenerate sequences in transposable elements to identify novel transposon insertions	Highly efficient method for capturing known and unknown insertion sites	Extensive validation is needed to confirm insertion sites, due to presence of false-positive signals	(10,14)
	RC-Seq	DNA is fragmented and transposon-containing fragments are captured using hybridization to transposon-specific probes	Captures full-length transposon-containing loci	Extensive validation is needed to confirm insertion sites, due to presence of false-positive signals	(19)
	Panel sequencing	Capture a set of specified loci of interest using array-based	Can sequence relevant loci at ultra-high depth, providing accurate estimates of even low-level mosaicism	Information at loci not represented on the panel is lost	(11,26–31)

Single-cell genome amplification, the use of deep sequencing of bulk DNA and techniques used to profile specific regions of the genome are described. Abbreviations: MDA, multiple displacement amplification; DOP-PCR, degenerate oligonucleotide primer polymerase chain reaction; L1IP, LINE1 insertion profiling; RC-Seq, retrotransposon capture sequencing. Information regarding each technique obtained from references in the table, as well as (92) and (32).