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genotyping & screening
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genotyping & screening

NovoHelix offers a range of cell screening services to ensure success of custom ‘disease-in-a-dish’ cell models.   These service requests include karyotyping to ensure normal ploidy of stem cells lines, screening for adventitious pathogens like mycoplasma and viruses, cell line authentication via short-tandem repeat profiling, and colony screening in 96-well or 384-well microplate formats for a targeted allele after homologous recombination of a gene targeting vector.  Although we have not enumerated every cell screening service that we offer, please inquire through our online quote portal for requests that are not directly listed.
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services

Service

Catalog Nr

Service Description

Price

 cell line authentication, STR profile
CMGS001

 Short-tandem repeat profiling of human cell lines is an easy-to-use way to authenticate/ confirm the identity of your cells. STR profiling aids in the detection of misidentified, cross-contaminated, or genetically drifted cells, which invalidate research results. Our STR analysis meets all requirements for funding, publication, and quality control. 

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 cell line authentication, species profile
 CMGS002
NovoHelix COI Assay is used to reliably determine the species of a cell line


The use of cytochrome C oxidase I (COI) testing at NovoHelix replaces isoenzymology in determining the true species of a cell line. The cytochrome C oxidase I gene (COI) is conserved genetic material found in the mitochondria among closely related species and across diverse phyla in the animal kingdom. 2* Based on the species-to-species sequence variability of the COI gene, NovoHelix scientists developed a PCR-based speciation assay by designing unique primer pairs that recognize only a specific species and produce amplicons in a multiplex PCR reaction with sizes no less than 20 base pairs apart.1 The NovoHelix COI assay is capable of distinguishing cell lines of pig, human, cat, Chinese hamster, Rhesus monkey, sheep, horse, African green monkey, rat, dog, mouse, rabbit, goat and cow origin. When the species of a cell line remains in question a ~650bp ‘barcode’ region of the COI gene is sequenced for verification purposes.
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 Mycoplasma detection, PCR-based
 CMGS003
Rapid, Reproducible, Sensitive, Cost-Effective  Can detect a broad range of mycoplasma species, including non-culturable strains Mycoplasma is a serious contaminant found commonly in cell cultures in laboratories.  Cells contaminated by mycoplasma may have compromised growth, morphology, physiology and even chromosomal aberrations. Such adverse changes are likely to affect the reliability of experiments that use these contaminated cells. Routine Tests to check for mycoplasma are therefore an important and necessary quality control procedure for all cell culture labs.  NovoHelix’s PCR Mycoplasma Detection Kit was designed to identify a conserved rRNA coding region in the mycoplasma genome, enabling it to detect majority of the mycoplasma species. It is an affordable, fast, and sensitive method for routine monitoring of mycoplasma-free cell cultures. The internal control designed in the kit eliminates false negatives and provides highly reliable results. This all-inclusive PCR Mycoplasma Detection Kit can be used in conjunction with a secondary detection method such as cell culture isolation, ELISA, etc.


Mycoplasma species detected:


M. pneumoniae, M. mycoides, M. capricolum, M. hyorhinis, M. hyopneumoniae, M.canis, M. genitalium, M. ovipneumoniae, M. flocculare, M. yeatsii, M.putrefaciens, M. synoviae, M. hominis, M. pirum, M. arginine, M. bovoculi, M. crocodyli, M.penetrans, M. arthritidis, M. salivarium, M. cynos, M. conjunctivae, M. dispar, M. canadense

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 Pathogen + Mycoplasma testing of client-provided ES cell lines
 CMGS004
Screening for adventitious pathogens including mycoplasma and viruses.

Human virus screen includes:
CMV, cytomegalovirus; EBV, Epstein-Barr virus; HHV-6, human herpesvirus 6; HHV-7, human herpesvirus 7; BKV, human polyomavirus BK; JCV, human polyomavirus JC; ADV, human adenovirus; B19V, human parvovirus B19; HBV, hepatitis B virus; HTLV-1, human T-cell leukaemia virus type 1; HTLV-2, human T-cell leukaemia virus type 2; HIV-1, human immunodeficiency virus 1; HIV-2, human immunodeficiency virus 2; HAV, hepatitis A virus; HCV, hepatitis C virus. Human adenovirus subtypes screened include 1, 2, 3, 5, 6, 7, 8, 10, 11, 12, 16, 17, 19, 21, 28, 31, 34, 40 and 48.


Mycoplasma species detected:
M. pneumoniae, M. mycoides, M. capricolum, M. hyorhinis, M. hyopneumoniae, M.canis, M. genitalium, M. ovipneumoniae, M. flocculare, M. yeatsii, M.putrefaciens, M. synoviae, M. hominis, M. pirum, M. arginine, M. bovoculi, M. crocodyli, M.penetrans, M. arthritidis, M. salivarium, M. cynos, M. conjunctivae, M. dispar, M. canadense
 Mycoplasma testing of client-provided ES cell clones
CMGS005
 Chromosome counting ($350 per clone)
CMGS006

Service request includes chromosome counting of a minimum of 20 metaphase spreads, a summary of findings, and 2 karyotype images representative of the cell line.  We will report abnormal events observed including trisomies, monosomies, deletions, insertions, translocations, duplications, endoreduplications, and other aberrations. 

 Genotyping Assay Development
CMGS007

Robust, transferable genotyping assays are needed to screen many of the animal and cellular models during our production and validation cycles. NovoHelix provides expert assay design and consultation to the client to ensure genotyping success.  Assay design costs are based on the number of alleles screened. In some cases, a synthetic positive control needs to be built for assay validation and these 'building' costs will be passed on to the client.


Service request includes chromosome counting of a minimum of 20 metaphase spreads, a summary of findings, and 2 karyotype images representative of the cell line.  We will report abnormal events observed including trisomies, monosomies, deletions, insertions, translocations, duplications, endoreduplications, and other aberrations. 
 Sample Genotyping
CMGS008
 Genotyping includes DNA extraction and purification services with a minimum charge of 10 samples. Samples that require additional genotyping validation such as Sanger sequencing of frameshifting mutants or point mutations will incur additional fee schedules (sequencing costs, etc). Genotyping is $15 per sample per allele screened.
technology
references
Huang J, Mirel D, Pugh E, Xing C, Robinson PN, Pertsemlidis A, Ding L, Kozlitina J, Maher J, Rios J, Story M, Marthandan N, Scheuermann RH. Minimum Information about a Genotyping Experiment (MIGEN). Stand Genomic Sci. 2011 Nov 30;5(2):224-9. doi: 10.4056/sigs.1994602. Epub 2011 Nov 22. PubMed PMID: 22180825; PubMed Central PMCID: PMC3235517.



Truett GE, Heeger P, Mynatt RL, Truett AA, Walker JA, Warman ML. Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT). Biotechniques. 2000 Jul;29(1):52, 54. PubMed PMID: 10907076.


Tunster SJ. Genetic sex determination of mice by simplex PCR. Biol Sex Differ. 2017 Oct 17;8(1):31. doi: 10.1186/s13293-017-0154-6. PubMed PMID: 29041956; PubMed Central PMCID: PMC5645908.


Hrovatin K, Kunej T. Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization. Ecol Evol. 2017 Dec 13;8(2):1009-1018. doi: 10.1002/ece3.3707. eCollection 2018 Jan. PubMed PMID: 29375774; PubMed Central PMCID: PMC5773321.


Strah R, Kunej T. Molecular sexing assays in 114 mammalian species: In silico  sequence reanalysis and a unified graphical visualization of diagnostic tests. Ecol Evol. 2019 Apr 8;9(8):5018-5028. doi: 10.1002/ece3.5093. eCollection 2019 Apr. Review. PubMed PMID: 31031962; PubMed Central PMCID: PMC6476764.


Green MR, Sambrook J. One-Tube Isolation of DNA from Mouse Tails. Cold Spring  Harb Protoc. 2018 Feb 1;2018(2). doi: 10.1101/pdb.prot093534. PubMed PMID: 29438056.


Weeks DP, Beerman N, Griffith OM. A small-scale five-hour procedure for isolating multiple samples of CsCl-purified DNA: application to isolations from mammalian, insect, higher plant, algal, yeast, and bacterial sources. Anal Biochem. 1986 Feb 1;152(2):376-85. PubMed PMID: 3963370.


Gemmell NJ, Akiyama S. An efficient method for the extraction of DNA from vertebrate tissues. Trends Genet. 1996 Sep;12(9):338-9. PubMed PMID: 8855658.


 Strauss WM. Preparation of genomic DNA from mammalian tissue. Curr Protoc Mol Biol. 2001 May;Chapter 2:Unit2.2. doi: 10.1002/0471142727.mb0202s42. PubMed PMID:18265182.

Behringer R, Gertsenstein M, Nagy KV, Nagy A. Isolation of High-Molecular-Weight DNA from Mouse Tail Tips. Cold Spring Harb Protoc. 2019 Apr 1;2019(4). doi: 10.1101/pdb.prot092692. PubMed PMID: 30936380.
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