Why Praxis Genomics? Unlike most other laboratories that use microarray to confirm NIPT results, we do this test using WGS for a similar cost. This allows upgrades to Exome, Expanded Exome, and Whole Genome Sequencing from the same dataset with the additional cost only being the difference between the respective tests. These include:

The Praxis Genomics Technology: This technique is used to obtain sequence from the entire genome of the patient which consists of about 3 billion units. For understanding the scope of this study, remember that the average human life is about 3 billion seconds long. This is accomplished without the use of any targeted enrichment of specific areas which eliminates the number of false positive and false negative results seen in panel and exome studies.

Easy to read reports: All this information is filtered and interpreted by a medical doctor. An easy-to-understand, concise report is issued with a clear diagnosis, allowing prognostication and choosing the best possible therapy for the patient.

Limitations of the method:

We accept amniotic fluid, chorionic villi, products of conception, and peripheral blood samples for this test. Please consult with support@praxisgenomics.com before sending samples to discuss shipping and turnaround time.

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Sample Types: With rare exceptions, in constitutional disorders all cells in the patient’s body carry the same disease causing DNA variant(s). This is the reason that these disorders can be diagnosed from different sample types such as blood, saliva, buccal swab, tissue biopsies from any organ or cultured cells. However, the best source is fresh blood since that can also be used for optical genome mapping in case additional testing is required.

Why Praxis Genomics? Our Basic Exome test is based on Whole Genome Sequencing (SRG). That means that we obtain sequence for the entire genome of the patient which minimizes the number of false positive and false negative results seen in capture-based panel and exome studies and allows us to report out all known pathogenic variants irrespective of their location. Basic Exome is defined as coding regions +/- 100bps plus mitochondrial genome (SNV, deletions) and single exon resolution CNV calling over coding regions.

Financial considerations: This test can be upgraded to Expanded Exome (SRG505) or Whole Genome Sequencing (SRG506) and Optical Genome Mapping (OGM001-004) and combined tests (PRX001-004) without providing additional patient sample. Upon upgrade only the difference in the price of the tests has to be paid. This arrangement lightens the burden of the patient and yet accelerates the time to diagnosis.

Easy to read reports: All information is filtered and interpreted by a board certified surgical and molecular genetic pathologist. An easy-to-understand, concise report is issued with a clear diagnosis, allowing prognostication and choosing the best possible therapy for the patient.

Limitations of the method: The method is limited to coding regions, exons, that are of particular interest to the patient and physician. The cause of the disease might be outside these regions. Repeat expansions, genomic losses, gains and rearrangements that do not result in loss of coding regions such as inversions, translocations cannot be detected. Duplications, while detectable, cannot be classified as tandem or inverted, and the genomic location for the duplicated fragment cannot be established.

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

For this test we obtain sequence from high molecular weight DNA for the entire genome of the patient but only report out regions of particular interest to the patient. This is accomplished without the use of any targeted enrichment of specific areas which minimizes the number of false positive and false negative results seen in capture-based panel and exomes studies. Using the Dragen alignment and variant calling pipeline, we can identify:

1. Single Nucleotide Variants (SNVs) and small insertions and deletions (InDels) in the nuclear and mitochondrial genome
2. Known pathogenic variants are reported irrespective of their localization in the genome
3. High resolution copy number changes (CNVs) within 100s of base pairs depending on the specific region
4. Repeat expansion disorder screening

Limitations of the method:

1. The method is limited to regions that are of particular interest to the patient and the ordering physician. The cause of the disease might be outside these regions. For this reason, in case of a negative report we allow for upgrade to genome testing for a fee, but without the need for additional sample submission.
2. Genomic rearrangements that do not result in loss of genetic material cannot be identified using short read technology alone. Such changes include inversions, when a fragment of DNA is broken out and reannealed in the opposite direction, and translocations, when a piece of DNA is transferred from its normal location on the chromosome to another location. Duplications, while detectable, cannot be classified as tandem or inverted, and the genomic location for the duplicated fragment cannot be established with certainty. The best approach to correct this deficiency is to use Bionano optical genome mapping in conjunction with Illumina short read whole genome sequencing and transcriptome data. For this reason we allow upgrade to OGM testing without providing additional material.
3. The method does not provide precise sizing of repeats; sizing has to be done with alternative methodology.
4. Longer repeats (1000s of base pairs) also cannot be sized accurately using this technology. One important example is the characterization of the FSHD locus. This deficiency again can be remedied by using this method in conjunction with Bionano optical genome mapping. The test can be updated with Bionano testing for a fee, but without the need for additional sample submission.

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Why Praxis Genomics? Unlike most other laboratories that only report out small variants, we identify all types of variants detectable by short read technology. These include:

The Praxis Genomics Technology: This technique is used to obtain sequence from the entire genome of the patient which consists of about 3 billion units. For understanding the scope of this study, remember that the average human life is about 3 billion seconds long. This is accomplished without the use of any targeted enrichment of specific areas which eliminates the number of false positive and false negative results seen in panel and exome studies.

Easy to read reports: All this information is filtered and interpreted by a medical doctor. An easy-to-understand, concise report is issued with a clear diagnosis, allowing prognostication and choosing the best possible therapy for the patient.

Limitations of the method:

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Sample Types: All cells in the patient's body carry the same DNA variant(s) detected in this test. However, OGM requires extraction of ultrahigh molecular weight DNA and because of this requirement testing can be performed on either fresh blood, cultured cells or tissue biopsy. Saliva, buccal swab or formalin fixed samples cannot be used for OGM.

Why Praxis Genomics? Our laboratory is one of a few laboratories performing OGM as a clinical test in the world. The method is based on barcoding high molecular weight individual DNA molecules, 200,000 base pair-long or longer. Each DNA fragment has a unique barcode pattern depending on its sequence, that partially overlaps with the pattern of other fragments. From these partially overlapping long DNA fragments, an entire barcoded genome can be assembled. Comparison of this assembly with a known reference barcode pattern calculated based on the reference sequence can detect increased distances between bars or altered order of bars, that correspond to altered genomic architecture. These types of changes can have major functional consequences and thus disease causing potential and can be identified reliably with Optical Genome Mapping only.

Limitations of the method: The barcode is established by attachment of fluorescent molecules to DNA in a sequence specific manner. The bars are spaced on average about 1,000bp apart from each other, but the exact distance varies depending on the region. For this reason, the resolution of this method is about 1,000 bp in most areas, but there are some areas where it is higher or lower. The method is best performed in conjunction with whole genome sequencing which allows precise identification of breakpoints associated with structural variants.

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Why Praxis Genomics? Unlike most other laboratories that only report out small variants, long read sequencing can identify all types of variants not easily detectable by short read technology. These include:

The Praxis Genomics Technology: This technique is used to obtain sequence from the entire genome of the patient which consists of about 3 billion units. For understanding the scope of this study, remember that the average human life is about 3 billion seconds long. This is accomplished without the use of any targeted enrichment of specific areas which eliminates the number of false positive and false negative results seen in panel and exome studies.

Easy to read reports: All this information is filtered and interpreted by a medical doctor. An easy-to-understand, concise report is issued with a clear diagnosis, allowing prognostication and choosing the best possible therapy for the patient.

Limitations of the method:

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Why Praxis Genomics? Unlike most other laboratories that only report out DNA sequence changes, this test allows Praxis Genomics to also assess the methylation status and thus expression of genes across the genome. The test is performed using Oxford Nanopore technologies (ONT) and relies on direct identification of modified residues without the need for chemical (bisulfite) treatment. Long read sequencing can identify all types of variants not easily detectable by short read technology. These include:

The Praxis Genomics Technology: This technique is used to obtain sequence from the entire genome of the patient which consists of about 3 billion units. For understanding the scope of this study, remember that the average human life is about 3 billion seconds long. This is accomplished without the use of any targeted enrichment of specific areas which eliminates the number of false positive and false negative results seen in panel and exome studies.

Easy to read reports: All this information is filtered and interpreted by a medical doctor. An easy-to-understand, concise report is issued with a clear diagnosis, allowing prognostication and choosing the best possible therapy for the patient.

Limitations of the method:

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Sample Types: With rare exceptions, in constitutional disorders all cells in the patient's body carry the same disease causing DNA variant(s). This is the reason that genetic disorders can be diagnosed from different sample types such as blood, saliva, buccal swab, tissue biopsies from any organ or cultured cells. However, for the transcriptome analysis the tissue type has to be carefully evaluated since not all genes are expressed in all tissues. With that caveat, both fresh and formalin fixed (FFPE) samples can be used for transcriptome analysis.

Why Praxis Genomics? Only Praxis Genomics offers clinical transcriptome testing in the world. We consider it an essential tool for functional assessment of previously unclassified or undescribed variants detected by Whole Genome Sequencing or Optical Genome Mapping. Indeed, transcriptome analysis provides us an integrated readout of the changes in DNA and allows us to interpret the significance of such changes based on their functional effects.

Easy to read reports: All this information is filtered and interpreted by a board certified surgical and molecular genetic pathologist. An easy-to-understand, concise report is issued with a clear diagnosis, allowing prognostication and choosing the best possible therapy for the patient.

Limitations of the method: Transcriptome studies are sensitive to the type of cell or tissue they are performed on, and they are most effective if used in a targeted manner in conjunction with the whole genome sequencing and optical genome mapping data of the patient.

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Sample Types: With rare exceptions, in constitutional disorders all cells in the patient's body carry the same disease causing DNA variant(s). This is the reason that these disorders can be diagnosed from different sample types such as blood, saliva, buccal swab, tissue biopsies from any organ or cultured cells. However, for the OGM component of the test only fresh blood or tissue is acceptable.

Why Praxis Genomics? Currently only Praxis Genomics offers co-analysis and co-interpretation of OGM, SRG and SRT data. These datasets correspond to a high level overview, high resolution assessment, and functional assessment of the human genome. The complementary strength of these methodologies provides us with unparalleled diagnostic sensitivity and accuracy based on detection and reporting of the following types of variants:

Easy to read reports: All this information is filtered and interpreted by a medical doctor. An easy-to-understand, concise report is issued with a clear diagnosis, allowing prognostication and choosing the best possible therapy for the patient.

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Sample Types: With rare exceptions, in constitutional disorders all cells in the patient's body carry the same disease causing DNA variant(s). This is the reason that FSHD2 can be diagnosed from different sample types such as blood, saliva, buccal swab, tissue biopsies from any organ or cultured cells. However, FSHD1 testing performed using optical genome mapping requires fresh blood.

Why Praxis Genomics? Praxis Genomics is the only laboratory in the USA that currently offers testing for FSHD1 and FSHD2 individually, as well as in combination. FSHD is a muscular dystrophy with a characteristic clinical presentation and very complex molecular pathogenesis. Rather than being caused by a single mutation, it arises from the combined effects of several genetic characteristics of the individual. In other words, changes that would cause disease in one person may not cause any or will cause only mild symptoms in another. This variation can be observed even within affected families. Prognostication of the disease and providing reproductive recommendations for affected individuals requires a precise genetic evaluation of the factors involved. Two main forms of the disease are described: FSHD1 and FSHD2. FSHD1 is the more common form, representing about 95 percent of all cases, while FSHD2 is suspected when the patient comes up negative for causes of FSHD1. Currently no single technology can characterize all the factors involved in pathogenesis for both types of FSHD. Optical Genome Mapping (OGM) can determine whether the patient has FSHD1 and whole genome sequencing can diagnose FSHD2.

Easy to read reports: All this information is filtered and interpreted by a board certified surgical and molecular genetic pathologist. An easy-to-understand, concise report is issued with a clear diagnosis, allowing prognostication and choosing the best possible therapy for the patient. The FSHD1 report will specify the number of D4Z4 repeats on both chromosome 4 and 10 and will provide the DUX4 allele type (stable, 4qA or unstable, 4qB) associated with these repeats. FSHD1 is diagnosed if on chromosome 4 the repeat number is equal or less than 10 and DUX4 allele is stable (4qA). The FSHD2 test report will provide a list of mutations, both single nucleotide changes and deletions that would cause disease in the presence of normal repeat numbers

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Sample Types: With rare exceptions, in constitutional disorders all cells in the patient's body carry the same disease causing DNA variant(s). However, repeat sizing performed using optical genome mapping requires fresh blood.

Why Praxis Genomics? Repeat expansions cause a diverse and ever-expanding number of diseases. Their manifestations are diverse not only because they affect different genes, but also because they can arise in different regions of genes. The longer the repeat expansion, the more pronounced the associated clinical phenotype. Repeat expansions can be identified using Whole Genome Sequencing. For accurate sizing of repeat expansions greater than 500bp, Optical Genome Mapping is the methodology of choice. OGM analyzes 250-300,000 bp long individual DNA molecules and can thus provide accurate measurements even for the biggest repeats such as those seen in Myotonic Dystrophy type 1, ALS (C9ORF72 associated), or Fragile X syndrome. Other disorders where OGM based repeat mapping can be helpful are Friedrich Ataxia, SCA8 (ATXN8), SCA2 (ATXN2), SCA10 (ATXN10), SCA7 (ATXN7), SCA36 (NOP56), SCA31 (BEAN31), FRA12A (DIP2B), and Familial Adult Myoclonic Epilepsy type 1 (SMAD12).

Financial considerations: It is important to note that OGM can size multiple repeats in a single experiment for a single charge.

Easy to read reports: The report will focus on the repeat expansion of interest, but if requested all repeat regions mentioned above can be commented on.

Limitations of the method: This sizing approach only works for genes where the expansion is expected to add more than 500bp to the normal length of the repeat.

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note:

Region of interest is amplified using PCR and sequenced using next generation sequencing.

All specimen containers received should be labeled with the patient's name, date of birth, and MRN / ID number. The collection date should be written prominently on the tube. At least two identifiers should be listed on specimen containers. Specimen deliveries are accepted Monday-Friday for all specimen types. Specimen integrity will be assessed upon receipt and any discrepancies will be noted and communicated back to the provider. Sample containers must be shipped in IATA UN3373 Compliant Packaging. See the link below for Shipping Resources to learn more.

Please Note: