Congenital Hypothyroidism and Thyroid Hormone Resistance Sequencing Panel

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
1989 DUOX2 81479 Add to Order
DUOXA2 81479
FOXE1 81479
GLIS3 81479
GNAS 81479
HESX1 81479
IGSF1 81479
IYD 81479
NKX2-1 81479
NKX2-5 81479
PAX8 81479
POU1F1 81405
PROP1 81404
SECISBP2 81479
SLC16A2 81405
SLC26A4 81406
SLC5A5 81479
TG 81479
THRA 81479
THRB 81405
TPO 81479
TRH 81479
TRHR 81479
TSHB 81479
TSHR 81479
UBR1 81479
Full Panel Price* $1940.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1989 Genes x (26) $1940.00 81404, 81405(x3), 81406, 81479(x21) Add to Order
Pricing Comment

If you would like to order a subset of these genes contact us to discuss pricing.

Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Most cases of congenital hypothyroidism (CH) don't have an identifiable cause, but in about 10%-15% of cases the conditions are caused by pathogenic variants in genes associated with thyroid gland development and function. The majority of cases (~80%) are due to pathogenic variants in genes associated with thyroid dysgenesis (TSHR, PAX8, NKX2-1, FOXE1 and NKX2-5). The remaining ~15% are caused by defects in one of thyroid dyshormonogenesis-related genes (SLC26A4, SLC5A5, TPO, TG, IYD, DUOXA2, and DUOX2). Other causes appear to be very rare, including central hypothyroidism (TSHB, IGSF1, TRHR, THR and GNAS) and thyroid hormone resistance (THRA and THRB) (Péter and Muzsnai 2011; Nettore et al. 2013; Grasberger and Refetoff 2011). Over 85% of cases of thyroid hormone resistance (THR) are caused by THRB pathogenic variants. THRA pathogenic variants are a rare cause of THR (van Mullem et al. 2014; Tylki-Szymanska et al, 2015).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 DUOX2$690.00 81479 Add to Order
DUOXA2$690.00 81479
FOXE1$690.00 81479
GLIS3$690.00 81479
GNAS$690.00 81479
HESX1$690.00 81479
IGSF1$690.00 81479
IYD$690.00 81479
NKX2-1$690.00 81479
NKX2-5$690.00 81479
PAX8$690.00 81479
PROP1$690.00 81479
SLC16A2$690.00 81479
SLC26A4$690.00 81479
SLC5A5$690.00 81479
TG$690.00 81479
THRA$690.00 81479
THRB$690.00 81479
TPO$690.00 81479
TRH$690.00 81479
TSHB$690.00 81479
TSHR$690.00 81479
UBR1$690.00 81479
Full Panel Price* $1290.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (23) $1290.00 81479(x23) Add to Order
Pricing Comment

# of Genes Ordered

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Over 100

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Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

One gross deletion of the entire NKX2-5 gene was reported to be causative for congenital heart defects (Glessner et al. 2014).

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Clinical Features

Congenital hypothyroidism (CH) is the most common congenital endocrine disorder. It occurs in one of every 3,000-4,000 newborns and is twice as common in females as in males. Without early and adequate treatment, CH is characterized by growth failure, developmental delay, and permanent intellectual disability. Current newborn screening primarily detects the elevated thyroid stimulating hormone (TSH) level at birth in response to decreased or absent thyroid hormone production and can identify over 90% of CH cases. Most CH patients grow and develop normally after treatment with thyroxine (Park and Chatterjee 2005; Rose et al. 2006). CH is usually a sporadic disorder, but growing evidence confirms several genetic mechanisms together account for at least 10% of cases. The majority of CH cases (~80%) are due to developmental defects of the thyroid gland known as thyroid dysgenesis, including thyroid agenesis, hypoplasia, and ectopy. The remaining ~15% are caused by defects in one of the steps of thyroid hormone biosynthesis (thyroid dyshormonogenesis). Other less common causes are central hypothyroidism (impaired hypothalamic-pituitary-thyroid axis), thyroid hormone transporter defects, and thyroid hormone resistance (Peter and Muzsnai 2011; Nettore et al. 2013; Weber et al. 2013; Grasberger and Refetoff 2011). Thyroid hormone resistance (THR) is a rare genetic disorder caused by reduced tissue responsiveness to thyroid hormone. The estimated prevalence is about 1:40,000 births. The characteristic biochemical findings in patients with THR are elevated serum free thyroid hormone levels accompanied by nonsuppressed thyroid stimulating hormone production (Dumitrescu et al. 2013). The clinical presentation is highly variable and has a mixture of hypothyroidism and hyperthyroidism because of variable peripheral resistance among individuals as well as among different tissues within a single patient. Goiter is found in 66-95% of reported cases. Symptoms related to hypothyroidism include learning disabilities, delayed growth and bone development. Hyperactivity and tachycardia are associated with high thyroid hormone levels. In the mild form of THR, isolated biochemical abnormalities may be the only findings (Dumitrescu et al. 2013; Ferrara et al. 2012; Amor et al. 2014). A defect in the thyroid hormone receptor beta gene (THRB) accounts for almost 85% of THR cases. Heterozygous pathogenic variants in the thyroid hormone receptor alpha gene (THRA) lead to a rare form of THR with congenital hypothyroidism as the predominant clinical presentation (van Mullem et al. 2014).


This NextGen test analyzes 26 genes leading to monogenic forms of congenital hypothyroidism and/or thyroid hormone resistance. Thyroid disorders listed below are inherited as autosomal dominant (PAX8, NKX2-1, NKX2-5, GNAS, and THRA) or recessive (SLC26A4/PDS, SLC5A5/NIS, TPO, TG, IYD/DEHAL1, DUOXA2, TSHB, SECISBP2, GLIS3, FOXE1, TRHR, PROP1 and UBR1), or X-linked (IGSF1 and SLC16A2) conditions. TSHR, POU1F1, HESX1, DUOX2, or THRB -associated diseases can present with either dominant or recessive patterns of inheritance (Péter and Muzsnai 2011; Grasberger and Refetoff 2011, Dumitrescu et al. 2013; Nettore et al. 2013). Primary thyrotropin-releasing hormone deficiency is expected to be caused by loss of function TRH variants. However, no pathogenic variants have been reported so far to be causative for primary TRH deficiency (Mori et al. 1991; Prieto-Tenreiro et al. 2010).

Thyroid dysgenesis: TSHR, PAX8, NKX2-1, FOXE1 and NKX2-5

Thyroid dyshormonogenesis: SLC26A4/PDS, SLC5A5/NIS, TPO, TG, IYD/DEHAL1, DUOXA2, and DUOX2

Central hypothyroidism: TSHB, IGSF1, TRH, TRHR and GNAS

Abnormal thyroid hormone metabolism: SECISBP2

Thyroid hormone resistance: THRA and THRB

Congenital hypothyroidism and neonatal diabetes mellitus: GLIS3

Pituitary hormone deficiency, combined: POU1F1, PROP1 and HESX1

Johanson-Blizzard syndrome: URB1

Allan-Herndon-Dudley syndrome: SLC16A2

See individual gene test descriptions for information on clinical features and molecular biology of gene products.

Testing Strategy

For this NGS panel, the full coding regions, plus ~20bp of non-coding DNA flanking each exon, are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization method, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, undocumented and questionable variant calls are confirmed by Sanger sequencing. Due to sequence homologies, exons 5-8 of the DUOX2 gene are analyzed via Sanger sequencing.

This panel provides 100% coverage of the aforementioned regions of the indicated genes. We define coverage as > 20X NGS reads for exons and 0-10 bases of flanking DNA, > 10X NGS reads for 11-20 bases of flanking DNA, or Sanger sequencing.

Indications for Test

Individuals with clinical symptoms consistent with hypothyroidism or thyroid hormone resistance and absence of anti-thyroid antibodies.


Name Inheritance OMIM ID
Allan-Herndon-Dudley Syndrome AR 300523
Choreoathetosis, Hypothyroidism, And Neonatal Respiratory Distress AD 610978
Diabetes Mellitus, Neonatal, With Congenital Hypothyroidism AR 610199
Hyperthyroidism, Familial Gestational AD 603373
Hyperthyroidism, Nonautoimmune AD 609152
Hypothryoidism, Congenital, Nongoitrous 4 AR 275100
Hypothyroidism, Central, and Testicular Enlargement XL 300888
Hypothyroidism, Congenital, Due To Thyroid Dysgenesis AD 218700
Hypothyroidism, congenital, nongoitrous, 1 AR 275200
Hypothyroidism, Congenital, Nongoitrous, 5 AD 225250
Hypothyroidism, Congenital, Nongoitrous, 6 AD 614450
Johanson-Blizzard Syndrome AR 243800
Pendred Syndrome AR 274600
Pituitary Hormone Deficiency, Combined 1 AD 613038
Pituitary Hormone Deficiency, Combined 2 AD,AR 262600
Pseudohypoparathyroidism Type 1A AD 103580
Pseudohypoparathyroidism Type 1B AD 603233
Pseudohypoparathyroidism Type 1C AD 612462
Pseudopseudohypoparathyroidism AD 612463
Septooptic Dysplasia XL 182230
Thyroid Cancer, Nonmedullary, 4 AD 616534
Thyroid Dyshormonogenesis 1 AR 274400
Thyroid Dyshormonogenesis 2A AR 274500
Thyroid Dyshormonogenesis 3 AR 274700
Thyroid Dyshormonogenesis 4 AR 274800
Thyroid Dyshormonogenesis 5 AR 274900
Thyroid Dyshormonogenesis 6 AR 607200
Thyroid Hormone Metabolism, Abnormal AR 609698
Thyroid Hormone Resistance, Generalized, Autosomal Dominant AD 188570
Thyroid Hormone Resistance, Generalized, Autosomal Recessive AR 274300
Thyroid Hormone Resistance, Selective Pituitary AD 145650
Thyrotropin-Releasing Hormone Deficiency AR 275120

Related Tests

GNAS-Related Disorders via the GNAS Gene
HESX1-Related Disorders via the HESX1 Gene
SECISBP2-Related Disorders via the SECISBP2 Gene
Allan-Herndon-Dudley Syndrome or Monocarboxylate Transporter 8 Deficiency via the SLC16A2 Gene
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Bamforth-Lazarus Syndrome via the FOXE1 Gene
Ciliopathy Sequencing Panel
Combined Pituitary Hormone Deficiency-2 (CPHD2) via the PROP1 Gene
Complex Hereditary Spastic Paraplegia Sequencing Panel with CNV Detection
Comprehensive Cardiac Arrhythmia Sequencing Panel
Comprehensive Cardiology Sequencing Panel with CNV Detection
Congenital Hypothyroidism (Central Hypothyroidism and Testicular Enlargement) via the IGSF1 Gene
Congenital Hypothyroidism (Thyroid Dysgenesis) via the NKX2-1/TTF1 Gene
Congenital Hypothyroidism (Thyroid Dysgenesis) via the PAX8 Gene
Congenital Hypothyroidism (Thyroid Dyshormonogenesis) via the DUOX2 Gene
Congenital Hypothyroidism (Thyroid Dyshormonogenesis) via the DUOXA2 Gene
Congenital Hypothyroidism (Thyroid Dyshormonogenesis) via the IYD/DEHAL1 Gene
Congenital Hypothyroidism (Thyroid Dyshormonogenesis) via the SLC5A5/NIS Gene
Congenital Hypothyroidism (Thyroid Dyshormonogenesis) via the TG Gene
Congenital Hypothyroidism (Thyroid Dyshormonogenesis) via the TPO Gene
Congenital Hypothyroidism (Thyroid Hormone Resistance) via the THRA Gene
Congenital Hypothyroidism (Thyroid Stimulating Hormone Deficiency) via the TSHB Gene
Congenital Hypothyroidism (Thyrotropin-Releasing Hormone Deficiency) via the TRH Gene
Congenital Hypothyroidism and Neonatal Diabetes Mellitus via the GLIS3 Gene
Disorders of Sex Development and Infertility Sequencing Panel with CNV Detection
Disorders of Sex Development Sequencing Panel with CNV Detection
Female Infertility Sequencing Panel with CNV Detection
Hereditary Spastic Paraplegia Comprehensive Sequencing Panel with CNV Detection
Hypoparathyroidism Sequencing Panel
Isolated Nonsyndromic Congenital Heart Defects via the NKX2-5 Gene
Johanson-Blizzard Syndrome via the UBR1 Gene
Male Infertility Sequencing Panel with CNV Detection
Pendred Syndrome and Deafness, Autosomal Recessive 4, with Enlarged Vestibular Aqueduct (DFNB4) via the SLC26A4 Gene
Pulmonary Fibrosis and Surfactant Dysfunction Disorders Sequencing Panel
Thyroid Hormone Resistance via the THRB Gene
X-Linked Intellectual Disability Sequencing Panel with CNV Detection


Genetic Counselors
  • Amor A.J. et al. 2014. Hormones. 13: 74-8. PubMed ID: 24722129
  • Dumitrescu A.M., Refetoff S. 2013. Biochimica Et Biophysica Acta. 1830: 3987-4003. PubMed ID: 22986150
  • Ferrara A.M. et al. 2012. The Journal of Clinical Endocrinology and Metabolism. 97: 1328-36. PubMed ID: 22319036
  • Glessner J.T. et al. 2014. Circulation Research. 115: 884-96. PubMed ID: 25205790
  • Grasberger H., Refetoff S. 2011. Current Opinion in Pediatrics. 23: 421-8. PubMed ID: 21543982
  • Mori M. et al. 1991. Journal of Internal Medicine. 229: 285-8. PubMed ID: 1901077
  • Nettore I.C. et al. 2013. Journal of Endocrinological Investigation. 36: 654-64. PubMed ID: 23698639
  • Park S.M., Chatterjee V.K. 2005. Journal of Medical Genetics. 42: 379-89. PubMed ID: 15863666
  • Péter F., Muzsnai A. 2011. Pediatric Clinics of North America. 58: 1099-115, ix. PubMed ID: 21981951
  • Prieto-Tenreiro A., Diaz-Guardiola P. 2010. Hormones. 9: 176-80. PubMed ID: 20687402
  • Rose S.R., et al. 2006. Pediatrics 117: 2290–303. PubMed ID: 16740880
  • Tylki-Szymanska A. et al. 2015. Journal of Medical Genetics. 52: 312-6. PubMed ID: 25670821
  • van Mullem A.A. et al. 2014. European Thyroid Journal. 3: 17-24. PubMed ID: 24847461
  • Weber G. et al. 2013. Journal of Endocrinological Investigation. 36: 261-6. PubMed ID: 23404134
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NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most cases, we are unable to determine the phase of sequence variants.  In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants due to somatic mosaicism is limited.  Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options

myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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