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The Molecular Karyotype of 25 Clinical-Grade Human Embryonic Stem Cell Lines.

Canham MA, Van Deusen A, Brison DR, De Sousa PA, Downie J, Devito L, Hewitt ZA, Ilic D, Kimber SJ, Moore HD, Murray H, Kunath T - Sci Rep (2015)

Bottom Line: The application of human embryonic stem cell (hESC) derivatives to regenerative medicine is now becoming a reality.A total of 15 unique copy number variations (CNVs) greater than 100 kb were detected, most of which were found to be naturally occurring in the human population and none were associated with culture adaptation.In addition, three copy-neutral loss of heterozygosity (CN-LOH) regions greater than 1 Mb were observed and all were relatively small and interstitial suggesting they did not arise in culture.

View Article: PubMed Central - PubMed

Affiliation: MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, UK.

ABSTRACT
The application of human embryonic stem cell (hESC) derivatives to regenerative medicine is now becoming a reality. Although the vast majority of hESC lines have been derived for research purposes only, about 50 lines have been established under Good Manufacturing Practice (GMP) conditions. Cell types differentiated from these designated lines may be used as a cell therapy to treat macular degeneration, Parkinson's, Huntington's, diabetes, osteoarthritis and other degenerative conditions. It is essential to know the genetic stability of the hESC lines before progressing to clinical trials. We evaluated the molecular karyotype of 25 clinical-grade hESC lines by whole-genome single nucleotide polymorphism (SNP) array analysis. A total of 15 unique copy number variations (CNVs) greater than 100 kb were detected, most of which were found to be naturally occurring in the human population and none were associated with culture adaptation. In addition, three copy-neutral loss of heterozygosity (CN-LOH) regions greater than 1 Mb were observed and all were relatively small and interstitial suggesting they did not arise in culture. The large number of available clinical-grade hESC lines with defined molecular karyotypes provides a substantial starting platform from which the development of pre-clinical and clinical trials in regenerative medicine can be realised.

No MeSH data available.


Related in: MedlinePlus

Duplications found in hESC lines that are present on the DGV.(A) Chromosome 6 ideograms from SNP array analysis of MasterShef3 revealed a 267 kb duplication near the telomere, which contained 3 genes, MLLT4, KIF25, and FRMD1. Duplications of this size, or greater, have been reported and annotated on the DGV with an estimated frequency of 2.82% in the human population. (B) A 144 kb duplication was observed on chromosome 12p13.31 of RC17 hESCs. This region contained two genes, SCL2A14 and SLC2A3, and is represented on the DGV (3.9% frequency in humans).
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f2: Duplications found in hESC lines that are present on the DGV.(A) Chromosome 6 ideograms from SNP array analysis of MasterShef3 revealed a 267 kb duplication near the telomere, which contained 3 genes, MLLT4, KIF25, and FRMD1. Duplications of this size, or greater, have been reported and annotated on the DGV with an estimated frequency of 2.82% in the human population. (B) A 144 kb duplication was observed on chromosome 12p13.31 of RC17 hESCs. This region contained two genes, SCL2A14 and SLC2A3, and is represented on the DGV (3.9% frequency in humans).

Mentions: Amongst the 15 large hESC CNVs, we found 10 had clear evidence of being present in healthy individuals. For example, a duplication of 267 kb on chromosome 6q27 observed in MasterShef3 containing 3 protein-encoding genes—MLLT4, KIF25, FRMD1—was represented on the DGV and has been reported in the healthy population at a frequency of over 1 in 50 individuals (Fig. 2A) 485153. RC17 hESCs harboured a single 144 kb duplication on chromosome 12p13.31 encompassing the SLC2A14 and SLC2A3 genes (Fig. 2B). Although this is close to the NANOG locus, we do not believe it confers a growth advantage since this CNV is commonly found (1 in 25) in healthy individuals395154. A 132 kb duplication on chromosome 12p11.21 was detected in both KCL033 and KCL040 hESC lines (Supplementary Fig. S1). This region does not contain any protein-coding genes, and there are at least 14 submissions of this duplication on the DGV3951535455. Man11, MasterShef2, and MasterShef7 also harboured genomic duplications of greater than 100 kb that are represented on the DGV (Supplementary Fig. S1). Man11 harboured a 220 kb gain on chromosome 15q25.3 that has been reported several times395156. This duplication contains one gene, AKAP13, and this CNV was not found in the sibling hESC line, Man12. One of the CNVs detected in MasterShef7, a 315 kb duplication present on chromosome 14q21.3, contains a single gene, MDGA, and this CNV is also present on the DGV51. A 572 kb gain on chromosome 17q21.31 encompassing 5 genes in MasterShef2 was also found to be present in the normal population at high frequency (9.8%)53.


The Molecular Karyotype of 25 Clinical-Grade Human Embryonic Stem Cell Lines.

Canham MA, Van Deusen A, Brison DR, De Sousa PA, Downie J, Devito L, Hewitt ZA, Ilic D, Kimber SJ, Moore HD, Murray H, Kunath T - Sci Rep (2015)

Duplications found in hESC lines that are present on the DGV.(A) Chromosome 6 ideograms from SNP array analysis of MasterShef3 revealed a 267 kb duplication near the telomere, which contained 3 genes, MLLT4, KIF25, and FRMD1. Duplications of this size, or greater, have been reported and annotated on the DGV with an estimated frequency of 2.82% in the human population. (B) A 144 kb duplication was observed on chromosome 12p13.31 of RC17 hESCs. This region contained two genes, SCL2A14 and SLC2A3, and is represented on the DGV (3.9% frequency in humans).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4660465&req=5

f2: Duplications found in hESC lines that are present on the DGV.(A) Chromosome 6 ideograms from SNP array analysis of MasterShef3 revealed a 267 kb duplication near the telomere, which contained 3 genes, MLLT4, KIF25, and FRMD1. Duplications of this size, or greater, have been reported and annotated on the DGV with an estimated frequency of 2.82% in the human population. (B) A 144 kb duplication was observed on chromosome 12p13.31 of RC17 hESCs. This region contained two genes, SCL2A14 and SLC2A3, and is represented on the DGV (3.9% frequency in humans).
Mentions: Amongst the 15 large hESC CNVs, we found 10 had clear evidence of being present in healthy individuals. For example, a duplication of 267 kb on chromosome 6q27 observed in MasterShef3 containing 3 protein-encoding genes—MLLT4, KIF25, FRMD1—was represented on the DGV and has been reported in the healthy population at a frequency of over 1 in 50 individuals (Fig. 2A) 485153. RC17 hESCs harboured a single 144 kb duplication on chromosome 12p13.31 encompassing the SLC2A14 and SLC2A3 genes (Fig. 2B). Although this is close to the NANOG locus, we do not believe it confers a growth advantage since this CNV is commonly found (1 in 25) in healthy individuals395154. A 132 kb duplication on chromosome 12p11.21 was detected in both KCL033 and KCL040 hESC lines (Supplementary Fig. S1). This region does not contain any protein-coding genes, and there are at least 14 submissions of this duplication on the DGV3951535455. Man11, MasterShef2, and MasterShef7 also harboured genomic duplications of greater than 100 kb that are represented on the DGV (Supplementary Fig. S1). Man11 harboured a 220 kb gain on chromosome 15q25.3 that has been reported several times395156. This duplication contains one gene, AKAP13, and this CNV was not found in the sibling hESC line, Man12. One of the CNVs detected in MasterShef7, a 315 kb duplication present on chromosome 14q21.3, contains a single gene, MDGA, and this CNV is also present on the DGV51. A 572 kb gain on chromosome 17q21.31 encompassing 5 genes in MasterShef2 was also found to be present in the normal population at high frequency (9.8%)53.

Bottom Line: The application of human embryonic stem cell (hESC) derivatives to regenerative medicine is now becoming a reality.A total of 15 unique copy number variations (CNVs) greater than 100 kb were detected, most of which were found to be naturally occurring in the human population and none were associated with culture adaptation.In addition, three copy-neutral loss of heterozygosity (CN-LOH) regions greater than 1 Mb were observed and all were relatively small and interstitial suggesting they did not arise in culture.

View Article: PubMed Central - PubMed

Affiliation: MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, UK.

ABSTRACT
The application of human embryonic stem cell (hESC) derivatives to regenerative medicine is now becoming a reality. Although the vast majority of hESC lines have been derived for research purposes only, about 50 lines have been established under Good Manufacturing Practice (GMP) conditions. Cell types differentiated from these designated lines may be used as a cell therapy to treat macular degeneration, Parkinson's, Huntington's, diabetes, osteoarthritis and other degenerative conditions. It is essential to know the genetic stability of the hESC lines before progressing to clinical trials. We evaluated the molecular karyotype of 25 clinical-grade hESC lines by whole-genome single nucleotide polymorphism (SNP) array analysis. A total of 15 unique copy number variations (CNVs) greater than 100 kb were detected, most of which were found to be naturally occurring in the human population and none were associated with culture adaptation. In addition, three copy-neutral loss of heterozygosity (CN-LOH) regions greater than 1 Mb were observed and all were relatively small and interstitial suggesting they did not arise in culture. The large number of available clinical-grade hESC lines with defined molecular karyotypes provides a substantial starting platform from which the development of pre-clinical and clinical trials in regenerative medicine can be realised.

No MeSH data available.


Related in: MedlinePlus