UKAi007-A

General

Cell Line
hPSCreg name	UKAi007-A
Cite as:	UKAi007-A (RRID:CVCL_A5MZ)
Alternative name(s)	P13_wt5, Patient 2 control 1
Cell line type	Human induced pluripotent stem cell (hiPSC)
Similar lines	UKAi007-B (P13_mut1, Patient 2 D816V 1) Donor's gene variants: PDGFRA, PDGFRA, RUNX1, RUNX1, RUNX1, RUNX1, KIT, KIT, ABL1, ABL1, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1, IDH1, IDH1, SRSF2, SRSF2 Donor diseases: systemic mastocytosis UKAi004-B (patient 1 control 2, P4_wt8) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi004-A (P4_wt4, patient 1 control 1) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi004-C (P4_mut13, patient 1 D816V 1) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi004-D (P4_mut28, patient 1 D816V 2) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi004-E (P4_mut30, patient 1 D816V 3) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi008-A (Patient 3 control 1, P15_wt37) Donor's gene variants: PDGFRA, PDGFRA, KIT, KIT, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1 Donor diseases: systemic mastocytosis UKAi008-B (Patient 3 control 2, P15_wt108) Donor's gene variants: PDGFRA, PDGFRA, KIT, KIT, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1 Donor diseases: systemic mastocytosis UKAi008-C (Patient 3 D816V 1, P15_mut131) Donor's gene variants: PDGFRA, PDGFRA, KIT, KIT, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1 Donor diseases: systemic mastocytosis GENYOi005-A (FPD/AML-PBMC-iPSC4F73) Donor's gene variants: RUNX1 Donor diseases: Familial platelet disorder with associated myeloid malignancy UKAi001-A (iPS1, hsc3_hiPS_11) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-B (iPS2, hsc3_hiPS_29) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-C (hsc3_hiPS_40, iPS3) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-A-1 (hsc3_hiPS_11_4, IRF8-/- iPS1) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-B-1 (hsc3_hiPS_29_23, IRF8-/- iPS2) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-C-1 (hsc3_hiPS_40_16_6, IRF8-/- iPS3) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis
Last update	1st March 2021
Notes	Toledo et al., Blood, ePub ahead of print, 2020 Dec 23
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Provider
Generator	Universitätsklinikum Aachen (UKA) Contact: Universitätsklinikum Aachen (UKA)
Owner	Universitätsklinikum Aachen (UKA)
Distributors	Universitätsklinikum Aachen (UKA)
Derivation country	Germany
External Databases
BioSamples	SAMEA8268471
Cellosaurus	CVCL_A5MZ
Wikidata	Q107117229
General Information
Publications	Toledo MAS et al. Nintedanib targets KIT D816V neoplastic cells derived from induced pluripotent stem cells of systemic mastocytosis. Blood. 2021 Apr 15;137(15):2070-2084.
* Is the cell line readily obtainable for third parties?	Yes Research use: allowed Clinical use: not allowed Commercial use: not allowed

Donor Information

General Donor Information

Sex

male

Age of donor (at collection)

90-94

Phenotype and Disease related information (Donor)

Diseases

A disease was diagnosed.

Systemic mastocytosis

Acute systemic mastocytosis (ASM) The donor bone marrow cells (primary sample) used for reprogramming and iPSC generation are heterogeneous and genetically mosaic. Therefore the two iPSC lines from this donor (UKAi007-A and UKAi007-B) have different allele frequencies than the primary sample for the mutations tested. Please see Table 1 of Toledo et al. 2021 for the allele frequencies of the primary sample and the iPSC lines.

The donor is a carrier of a disease-associated mutation and affected.

Stage

35% mast cell burden in bone marrow

Synonyms

Genetic variants

ABL1 (target)

Chromosome location

9q34.12

Nucleotide sequence variant in HGVS format

NM_007313.2:c.2173G>A

Protein sequence variant in HGVS format

NP_009297.2:p.Gly725Ser

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

RCV000119949.1

ASXL1 (target)

Chromosome location

20q11.21

Nucleotide sequence variant in HGVS format

NM_015338.6:c.2444T>C

Protein sequence variant in HGVS format

p.Leu815Pro

Is the variant homozygous or heterozygous?

Homozygous

dbSNP

rs6058694

IDH1 (target)

Chromosome location

2q34

Nucleotide sequence variant in HGVS format

NM_005896.2:c.532G>A

Protein sequence variant in HGVS format

NP_005887.2:p.Val178Ile

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

RCV000121207.1

KIT (target)

Chromosome location

4q12

Nucleotide sequence variant in HGVS format

NM_000222.3:c.2447A>T

Protein sequence variant in HGVS format

NP_000213.1:p.Asp816Val

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

VCV000013852.5

dbSNP

rs121913507

PDGFRA (target)

Chromosome location

4q12

Nucleotide sequence variant in HGVS format

NM_006206.6:c.1432T>C

Protein sequence variant in HGVS format

NP_006197.1:p.Ser478Pro

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

VCV000041794.4

dbSNP

rs35597368

RUNX1 (target)

Chromosome location

21q22.12

Nucleotide sequence variant in HGVS format

NM_001754:c.399G>A

Protein sequence variant in HGVS format

p.Met133Ile

Is the variant homozygous or heterozygous?

Heterozygous

SRSF2 (target)

Chromosome location

38.p13

Nucleotide sequence variant in HGVS format

NM_001195427.1:c.284_307del

Protein sequence variant in HGVS format

p.Pro95_Arg102del

Is the variant homozygous or heterozygous?

Heterozygous

dbSNP

rs766200080

TET2 (target)

Chromosome location

4q24

Nucleotide sequence variant in HGVS format

NM_001127208.2:c.3781C>T

Protein sequence variant in HGVS format

NP_001120680.1:p.Arg1261Cys

Is the variant homozygous or heterozygous?

Heterozygous

TET2 (target)

Nucleotide sequence variant in HGVS format

NM_001127208:c.3876C>G

Protein sequence variant in HGVS format

p.Ser1292Arg

Is the variant homozygous or heterozygous?

Heterozygous

TP53 (target)

Chromosome location

17p13.1

Nucleotide sequence variant in HGVS format

NM_000546.6:c.215C>G

Protein sequence variant in HGVS format

NP_000537.3:p.Pro72Arg

Is the variant homozygous or heterozygous?

Homozygous

ClinVar

VCV000012351.11

dbSNP

rs1042522

RUNX1 (target)

Nucleotide sequence variant in HGVS format

NM_001754:c.302_318del

Protein sequence variant in HGVS format

p.Val101Alafs*31

Is the variant homozygous or heterozygous?

Heterozygous

TET2 (target)

Nucleotide sequence variant in HGVS format

NM_001127208:c.4393C>T

Protein sequence variant in HGVS format

p.Arg1465Ter

Is the variant homozygous or heterozygous?

Heterozygous

Karyotyping (Donor)

Has the donor karyotype been analysed?

No

Other Genotyping (Donor)

Is there genome-wide genotyping or functional data available?

No

Donor Relations

Other cell lines of this donor

UKAi007-B

External Databases (Donor)

BioSamples

SAMEA8268476

Ethics

Has informed consent been obtained from the donor of the embryo/tissue from which the pluripotent stem cells have been derived?	Yes
Was the consent voluntarily given?	Yes
Has the donor been informed that participation will not directly influence their personal treatment?	Yes
Can you provide us with a copy of the Donor Information Sheet provided to the donor?	No
Provide contact information of the holder of the original Donor Information Sheet:	Medical University of Vienna, Vienna, Austria
Do you (Depositor/Provider) hold the original Donor Consent Form?	No
If you do not hold the Donor Consent Form, do you know who does?	Yes
Contact information / weblink	Medical University of Vienna, Vienna, Austria
Alternatives to consent are available?	No
Is there other documentation provided to the donor for consenting purposes?	No
Confirm that consent was obtained by a qualified professional	Yes
Has the donor agreed to be re-contacted?	Unknown
Has the donor been informed about how her/his data will be protected?	Yes
Please indicate whether the data associated with the donated material has been pseudonymised or anonymised.	pseudonymised
Does consent explicitly allow the derivation of pluripotent stem cells?	Yes
Does consent expressly prevent the derivation of pluripotent stem cells?	No
Does consent pertain to a specific research project?	No
Does consent permit unforeseen future research, without further consent?	Yes
Does the consent permit uses of donated embryo/tissue or derived cell line intended for clinical treatment or human applications?	No
Does consent expressly prevent development of commercial products?	No
Does consent expressly prevent financial gain from any use of the donated embryo/tissue, including any product made from it?	No
Does consent expressly permit storage of donated embryo/tissue for an unlimited time?	Yes
Does consent expressly permit storage of cells derived from the donated embryo/tissue for an unlimited time?	Yes
Does consent prevent the DONATED BIOSAMPLE from being made available to researchers anywhere in the world?	No
Does consent prevent CELLS DERIVED FROM THE DONATED BIOSAMPLE from being made available to researchers anywhere in the world?	No
Does consent permit research by
an academic institution?	Yes
a public organisation?	Yes
a non-profit company?	Yes
a for-profit corporation?	Yes

Does consent expressly permit collection of genetic information?	Yes
Does consent expressly permit storage of genetic information?	Yes
Does consent prevent dissemination of genetic information?	Yes
Has the donor been informed that their donated biosample or derived cells may be tested for the presence of microbiological agents / pathogens?	No
Has the donor consented to receive information discovered during use of donated embryo/tissue that has significant health implications for the donor?	No
How may genetic information associated with the cell line be accessed?	Controlled Access
Will the donor expect to receive financial benefit, beyond reasonable expenses, in return for donating the biosample?	No
Does the consent anticipate that the donor will be notified of results or outcomes of any research involving the donated samples or derived cells?	No
Does the consent permit the donor, upon withdrawal of consent, to stop the use of the derived cell line(s) that have already been created from donated samples?	Yes
Does the consent permit the donor, upon withdrawal of consent, to stop delivery or use of information and data about the donor?	Yes
Does consent permit access to medical records of the donor?	No
Does consent permit access to any other source of information about the clinical treatment or health of the donor?	No
Has a favourable opinion been obtained from a research ethics committee, or other ethics review panel, in relation to the Research Protocol including the consent provisions?	Yes
Name of accrediting authority involved?	Medical University of Vienna ethics board, Vienna, Austria
Approval number	EK1184/2014
Has a favourable opinion been obtained from a research ethics committee, or other ethics review panel, in relation to the PROPOSED PROJECT, involving use of donated embryo/tissue or derived cells?	Yes
Name of accrediting authority involved?	Medical University of Vienna ethics board, Vienna, Austria
Approval number	EK1184/2014
Do you have obligations to third parties in regard to the use of the cell line?	No
Are you aware of any further constraints on the use of the donated embryo/tissue or derived cells?	No
Is there an MTA available for the cell line?	Yes
For generation of the cell line, who was the supplier of any recombined DNA vectors or commercial kits used?	Life Technologies
Are you aware of any constraints on the use or distribution of the cell line from the owner or any parties identified in the query above?	No

hIPSC Derivation

General
Source cell type	Bone Marrow The tissue occupying the spaces of bone. It consists of blood vessel sinuses and a network of hematopoietic cells which give rise to the red cells, white cells, and megakaryocytes. Synonyms BONE MARROW Bone Marrow Reticuloendothelial System, Bone Marrow bone marrow Bone marrow Bone marrow structure (body structure) Marrow medulla ossea medulla ossium show more synonyms show less synonyms
Source cell origin	Bone Marrow The tissue occupying the spaces of bone. It consists of blood vessel sinuses and a network of hematopoietic cells which give rise to the red cells, white cells, and megakaryocytes. Synonyms BONE MARROW Bone Marrow Reticuloendothelial System, Bone Marrow bone marrow Bone marrow Bone marrow structure (body structure) Marrow medulla ossea medulla ossium show more synonyms show less synonyms
Source cell type (free text)	CD117+ cells (MACS)
Age of donor (at collection)	90-94
Collected in	2016
Passage number reprogrammed	0
Reprogramming method
Vector type	Non-integrating
Vector	Sendai virus
Genes	POU5F1 SOX2 KLF4 MYC
Is reprogramming vector detectable?	Unknown
Vector free reprogramming
Other
Selection criteria for clones	ES cell like morphology
Derived under xeno-free conditions	No
Derived under GMP?	No
Available as clinical grade?	No

Culture Conditions

Surface coating

Gelatin

Feeder cells

mouse embryonic fibroblasts

Passage method

Enzymatically

Collagenase

O2 Concentration

21 %

CO2 Concentration

5 %

Medium

Other medium:

Base medium: Knock out DMEM
Main protein source: Knock-out serum replacement
Serum concentration: 20 %

Supplements

Supplement	Amount	Unit
bFGF	10	ng/ml

Has Rock inhibitor (Y27632) been used at passage previously with this cell line?

Yes

Has Rock inhibitor (Y27632) been used at cryo previously with this cell line?

Yes

Has Rock inhibitor (Y27632) been used at thaw previously with this cell line?

Yes

Characterisation

Analysis of Undifferentiated Cells

Marker Expression

Marker	Expressed	Immunostaining	RT-PCR	Flow Cytometry	Enzymatic Assay	Expression Profiles
NANOG	Yes
POU5F1 (OCT-4)	Yes
TRA 1-60	Yes
TRA 1-81	Yes

EpiPluriScore

Score: 0.23

Marker	Present	Absent
mCpG	X
OCT4	X

Microbiology / Virus Screening
HIV 1	Negative
HIV 2	Negative
Hepatitis B	Negative
Hepatitis C	Negative
Mycoplasma	Negative

Genotyping

Karyotyping (Cell Line)
Has the cell line karyotype been analysed?	Yes 46 XY Zellbio_WT_5_IV_003_K.TIF Karyotyping method: G-Banding
Other Genotyping (Cell Line)

P13_wt5, Patient 2 control 1

General

Cell Line

Provider

External Databases

General Information

Donor Information

General Donor Information

Phenotype and Disease related information (Donor)

ABL1 (target)

ASXL1 (target)

IDH1 (target)

KIT (target)

PDGFRA (target)

RUNX1 (target)

SRSF2 (target)

TET2 (target)

TET2 (target)

TP53 (target)

RUNX1 (target)

TET2 (target)

Karyotyping (Donor)

Other Genotyping (Donor)

Donor Relations

External Databases (Donor)

Ethics

Does consent permit research by

hIPSC Derivation

General

Reprogramming method

Vector free reprogramming

Other

Culture Conditions

Characterisation

Analysis of Undifferentiated Cells

Microbiology / Virus Screening

Genotyping

Karyotyping (Cell Line)

Other Genotyping (Cell Line)