ChrisR/current NextGenSeq testing

NGS comparison table

FGC = Full Genomes Corporation, FTDNA = Family Tree DNA, see also Y-DNA next generation sequencing, Y-DNA SNP testing chart and Autosomal DNA testing comparison chart.

	FGC WGS 30×	FGC WGS 20×	FGC WGS 15× (GenomeGuide)	FGC WGS 10×	FGC WGS 4×	1000 Genomes Ph.3	FGC WGS 2×	FGC Y-Elite 2	FGC Y-Elite 1	FTDNA BigY
Introduced	Summer 2014	Late 2015	Early 2016	July 2015	July 2015	2011-2013	July 2015	May 2015	Late 2012-2015	November 2013
Price	$1250 ($42/×)	$1200 ($60/×)	$895 ($60/×)	$725 ($73/×)	$395 ($99/×)	-	$280 ($140/×)	$775	$850-1299	$575
Sequenced DNA focus	whole genome	whole genome	whole genome	whole genome	whole genome	whole genome	whole genome	Y-DNA, mtDNA	Y-DNA, mtDNA	Y-DNA (until April 2015 mtDNA)
Read depth, read length, Method	30× 150 bp (or 10 mb)	20× 150 bp	15× 150 bp	10× 150 bp	4× 150 bp	min. 4×, av. 7× > 70bp	2× 150 bp	30× 250 bp	50× 100 bp	60× 100 bp
Upgrade options	$55 per 1× + $100 data fee	price difference + $100 data fee	price difference + $100 data fee	price difference + $100 data fee	price difference to 10× + $100 data fee	-	price difference to 4× + $100 data fee	2nd order for 60×	-	-
Y ≥1× coverage (FGC)	~22.9 mbp 92% hg19	~22.8 mbp 92% hg19	~ ?	~21.8 mbp 89% hg19	~17.7 mbp 72% hg19	? mbp	~13.8 mbp 56% hg19	>22.0 mbp 89% hg19	~22.8 mbp 92% hg19 (21.5-23 mbp)	~16 mbp 65% hg19 (14-23 mbp)
Y Callable Loci (GATK) (FGC qual.-read-lenght)	~14.9 mbp	~13.9 mbp	~13.2 mbp	~8.0 mbp	~1.1 mbp	?	~0.4 mbp	~14.8 mbp	~14.1 mbp	~8.8 mbp
Y Method Analysis (YFull)	Mean/Av. 21× Median 12× ~22.8 mbp ~0.3 Gb BAM ~2900? SNPs ?/111 STRs			Mean/Av. 10-11× Median 4-5× ~88% Y-cov-hg19 ~0.2 Gb BAM ~2,762 known + ? novel SNPs ~?/111 STRs	Mean/Av. 9× Median 4× ~87% Y-cov-hg19 ~0.1 Gb BAM 2,764 known + 243 novel SNPs ~81/111 STRs	Mean/Av. ?× Median ?× ? bp ~0.18 Gb BAM ~2300? SNPs ca. 1/3 of 111 STRs	?	Mean/Av. ~47-72× Median ~31-47× 22 mbp ~1.2 Gb BAM ~2750 SNPs ~107/111 STRs	Mean/Av. -76× Median 37-39× 22.7-25 mbp ~3 Gb BAM ~2800 SNPs ~98/111 STRs	Mean/Av. -91× Median 47-60× ~13.9 mbp ~0.8 Gb BAM ~2050 SNPs ~96/111 STRs
mt Method Analysis			~100% FMS Mean/Av. >1000X	~100% FMS Mean/Av. >1000X				92-100% FMS	~95% FMS Mean/Av. ~26X (75-100%)	~69% FMS Mean/Av. ~13-41X (0-100%)
at/X Method ~3,60 mill. SNPs expected	~3.60 mill. SNPs (~100%) ca. 22.5x? Coverage ca. 95%.		~3.52 mill. SNPs (~98%)	~3.11 mill. SNPs (~86%)	~1.75 mill. SNPs (~49%)			not included	not included	not included

Numbers of variants in the human genome / in WGS databases

The human nucleotide diversity is estimated to be 0.1% to 0.4% of base pairs. A difference of 1 to 4 in 1,000 amounts to approximately 3 to 12 million nucleotide differences, because the human genome has about 3 billion nucleotides.

SNVs and structural variation of some WGS databases (Francioli, Menelaou et al 2014)

Variants shared by whole genomes of 250 Dutch parent-offspring families from Genome of the Netherlands (GoNL) Project (20.4 million single-nucleotide variants and 1.2 million insertions and deletions, intermediate coverage ~13×)

Variant dataset	Variants M(illions)	percent
HapMap CEU 2005-2009	2.3	11%
1000G EUR 2011-2013	9.1	45%
1000G 2011-2013	1.2	6%
dbSNP 1998-2013	0.2	1%
GoNL 2014 only	7.6	37%
Sum	20.4	100%

See for comparison the widely used Illumina SNP chips (23andMe, FamilyFinder, Ancestry.com, etc.) which provide a few hundred thousand SNP Markers: Autosomal DNA testing comparison chart

relationship between read depth and coverage in Next generation sequencing (Wang, Wei et al 2011)

Minimal read depth and coverage for variant (SNV/SNP) research

Sequencing depth represents the (often average) number of nucleotides contributing to a portion of an assembly. On a genome basis, it means that, on average, each base has been sequenced a certain number of times (10×, 20×,...). For a specific nucleotide, it represents the number of sequences that added information about that nucleotide. Such depth varies quite a lot depending on the genomic region. In consequence, an average sequencing depth of 30× leaves a lot of small portions of a genome unsequenced while other receive a lot more sequences.

Low confidence: 7×

The 1000 Genomes Project sequenced genomes of 2,504 individuals representing 26 populations to an average of 7× coverage. This dataset is used by many for variant research and has acceptable minimal confidence for haploid genome parts (mtDNA and hemizygous Y-DNA).

accuracy variant calling various coverage depths (filtered on chr20, Cheng, Teo et al 2014)

Medium confidence: 10× - 59×

Everything >7× is called Deep sequencing. For detecting human genome mutations, SNPs, and rearrangements, publications often recommend from 10× to 30× depth of coverage, depending on the application and statistical model. A 2011 study calls 10× SNP calling capability enough for the standard SNP analysis evaluation.

Analysis of the first sequenced human genome in 2008 suggests that homozygous SNVs are detected at a 15× average depth and an average depth of 33× is required to detect the same proportion of heterozygous SNVs. A 2011 study suggests improvements in sequencing set the required average mapped depth to 35× for reliable calling of SNVs and small indels across 95% of the genome.

SNP call accuracy according to a 2014 study on single nucleotide variant detection and genotype calling (for chr20)

• 5×: 90-97%
• 10×: 96-98%
• 15×: 98% (Minimum for rare variants)
• ≥20×: 99%

Minimum depth for correct genotype call (Meynert, Ansari et al 2014)

High confidence: 60× and higher

• For high confidence of Exome variants (medical)
• "We calculated that 60× WGS data from the HiSeq 2000 platform are needed to recover ~95% of INDELs, much higher than that for SNP detection. Accurate detection of heterozygous INDELs requires ~1.2-fold higher coverage than that for homozygous INDELs"

Interesting features for population genetics and genetic genealogy

Enrichment / target designs can help to provide better coverage for certain genome areas. Ability to deliver the following data seems crucial for competitivity in the market:

Y

• Detection derived Y-SNPs > 2000
• Y-STR coverage especially for FTDNA Y37-Y67 panel
• FASTQ files for remapping possibility

Autosomal/X

• Coverage for the main DTC-chip SNPs useful for admixture and IBD comparisons like on Gedmatch: 23andMe (v1-v4), Ancestry.com, FTDNA FamilyFinder, Geno 2.0 (v1-v2), Chromo2;
• Phasing: possibility to distinguish paternal and maternal DNA in an individual without having parents DNA/testing. At 34× phasing of 96 % of SNPs into haplotype blocks should be already possible.
• Potential for coverage of highly informative continental and regional SNPs (rare variants) to be used in future admixture and matching services (distant genetic relations).

mt

• ~100% FMS with good mean read depth (>50×)