NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Table 1 Summary of individuals included in this study

Individual	ABCA7 VNTR lengths (kb)		DNA source	PromethION device	Sequencing chemistry	Number of flow cells	Yield (Gb)	Read length N50 (kb)
Subject01	5.1	4.5	QIAmp	α	108	6 + 7^d	74.4	7.0
Subject02	1.8	1.8	QIAmp	α	108	1	61.3	11.2
Subject03	4.7	2.3	QIAmp	α	109	1	72.5	16.3
Subject04	9.7	0.8	QIAmp	α	109	1	85.5	11.5
Subject05	10.7	1.7	QIAmp	α	109	1	88.5	11.9
Subject06	2.3	0.3	QIAmp	α	109	1	98.0	16.2
Subject07	3.3	3.3	Magtration	α	109	1	77.7	10.6
Subject08	2.3	0.4	Magtration	β	109	1	56.2	14.7
Subject09^a	5.5	4.3	Magtration	β	109	1	43.2	29.3
Subject10^b	8.7	2.8	Magtration	β	109	1	48.9	9.1
NA19240	4.5	2.2	Magtration	β	109^c	5	220.0	15.8

DNA was either extracted with QIAmp (Qiagen) or on a Magtration robotic platform (PSS). An alpha (α) and beta (β) PromethION device were used. Two chemistries were applied: SQK-LSK108 (108) or SQK-LSK109 (109). Yield and mean read length were calculated with NanoPack [23] after Albacore or Guppy base calling. kb kilobases, Gb gigabases, N50 50% of the total sequencing dataset is contained in reads equal or larger than this value. ^aDNA was not sheared for this individual. ^bAn 8-year-old DNA extraction was used. ^cSQK-LSK109 was used for four flow cells and for one flow cell was run with SQK-LSK108. ^dSix debug PromethION flow cells and seven MinION flow cells were used

ISSN: 1474-760X