Retinal Dystrophy Panel

Posted on by Dru Leistritz

The Retinal Dystrophy exome panel testing includes more than 200 genes that have been identified to be responsible for disorders in which retinal dystrophy is a noted feature:

Retinal Dystrophy Panel Gene List

Retinal Dystrophy exome panel testing is the most cost-efficient and precise approach to diagnostic testing as there is overlap between phenotypes and the lack of characteristic “other” features in many instances.   Study of the panel genes from the DNA of a single individual allows us to focus on variants reported as pathogenic in the past, on those with a very low population frequency, with nucleotide conservation across species and with likely pathogenic consequence. When variants of unknown significance are identified by panel testing, DNA is requested from first degree relatives to interrogate the significance of the variant. There is no charge for added studies used to aid in interpretation of a sequence change found in the index case.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.   The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

Neuromuscular Disorder Panels

Posted on by Melanie Pepin

The Neuromuscular Disorder Panels include genes that have been identified to be responsible for:
(Click link for gene list)

Spinal Muscular Atrophy

Charcot-Marie-Tooth and Neuropathies

Myopathies/Myotonia, Muscular Dystrophies and Limb Girdle Muscular Dystrophies

Myasthenic Syndromes and Arthrogryposis

Metabolic Myopathies Panel

Chronic Myopathies and Walker Warburg Syndrome

For the above panels order testing on any or all of the phenotypes relevant to your patient.  If none of the panels fit your testing needs, select up to six phenotypes from the Movement Disorder, Neurodegenerative Disorder, or Neuromuscular Disorder panels to create a custom panel.

Study of the panel genes from the DNA of a single individual allows us to focus on variants reported as pathogenic in the past, on those with a very low population frequency, with nucleotide conservation across species and with likely pathogenic consequence.  When variants of unknown significance are identified by panel testing, DNA is requested from first degree relatives to interrogate the significance of the variant.  There is no charge for added studies used to aid in interpretation of a sequence change found in the index case.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.  The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

Neurodegenerative Disorder Panels

Posted on by Melanie Pepin

The Neurodegenerative Disorder Panels includes genes that have been identified to be responsible for disorders in which neurodegeneration is a noted feature including:
(select panel below for gene list)

For the above panels order testing on any or all of the phenotypes relevant to your patient.  If none of the panels fit your testing needs, select up to six phenotypes from the Movement Disorder, Neurodegenerative Disorder, or Neuromuscular Disorder panels to create a custom panel.

Study of the panel genes from the DNA of a single individual allows us to focus on variants reported as pathogenic in the past, on those with a very low population frequency, with nucleotide conservation across species and with likely pathogenic consequence.  When variants of unknown significance are identified by panel testing, DNA is requested from first degree relatives to interrogate the significance of the variant.  There is no charge for added studies used to aid in interpretation of a sequence change found in the index case.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.   The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

 

Movement Disorder Panels

Posted on by Melanie Pepin

The four NCGL Movement Disorder Panels include genes that have been identified to be responsible for Ataxia, Hereditary Spastic Paraplegia, Dystonia and Choreatic Movement Disorders, and Parkinson’s Disease (select name of panel for gene list):

Ataxia Panel Gene List
Hereditary Spastic Paraplegia Panel Gene List
Dystonia and Choreatic Move Disorders Panel Gene List
Parkinson’s Disease Panel Gene List

 

For the above panels order testing on any or all of the phenotypes relevant to your patient.  If none of the panels fit your testing needs, select up to six phenotypes from the Movement Disorder, Neurodegenerative Disorder, or Neuromuscular Disorder panels to create a custom panel.

Study of the panel genes from the DNA of a single individual allows us to focus on variants reported as pathogenic in the past, on those with a very low population frequency, with nucleotide conservation across species and with likely pathogenic consequence.  When variants of unknown significance are identified by panel testing, DNA is requested from first degree relatives to interrogate the significance of the variant.  There is no charge for added studies used to aid in interpretation of a sequence change found in the index case.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.  The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

 

REFLEX to Exome Sequencing

Posted on by Melanie Pepin

For the patient with a particular phenotype in whom focused “panel” sequencing did not identify a pathogenic variant in NCGL, further evaluation of the completed NCGL exome sequence data is offered.   Review of the patient’s exome sequence file may be the most cost effective way of expanding gene sequence testing beyond presently known disease candidate genes.  Study of the exome from the DNA of a single individual is used to identify sequence variants with a very low population frequency, with nucleotide conservation across species and likely pathogenic consequence. Testing of a family trio facilitates filtering of sequence variants and reduces the number of potential candidates by looking for the same sequence alteration in an unaffected parent(s).

Comprehensive Cardiac Arrhythmia/Cardiomyopathy Panel

Posted on by Melanie Pepin

The Comprehensive Cardiac Arrhythmia/Cardiomyopathy Panel includes genes that have been identified to be responsible for disorders in which arrhythmia and/or cardiomyopathy are a noted feature:

Comprehensive Cardiac Arrhythmia and Cardiomyopathy Panel Gene List

Cardiac Arrhythmia disease phenotypes include Brugada syndrome, Familial atrial fibrillation, long QT, and arrhythmogenic right ventricular dysplasia among others.  Cardiomyopathy disease phenotypes include primary myopathies, muscular dystrophies; metabolic storage diseases, Noonan syndrome and cardiofaciocutaneous syndromes among others.  The Comprehensive Cardiac Arrhythmia/Cardiomyopathy exome panel is the most cost-efficient and precise approach to diagnostic testing as there is overlap between phenotypes and the lack of characteristic “other” features in many instances. Study of the panel genes from the DNA of a single individual allows us to focus on variants reported as pathogenic in the past, on those with a very low population frequency, with nucleotide conservation across species and with likely pathogenic consequence. When variants of unknown significance are identified by panel testing, DNA is requested from first degree relatives to interrogate the significance of the variant. There is no charge for added studies used to aid in interpretation of a sequence change found in the index case.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.   The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

Cardiomyopathy Panel

Posted on by Melanie Pepin

Cardiomyopathy exome panel testing includes over 70 genes that have been identified to be responsible for disorders in which cardiomyopathy is a noted feature:

Cardiomyopathy Panel Gene List

The disease phenotypes include primary myopathies, muscular dystrophies; metabolic storage diseases, Noonan syndrome and cardiofaciocutaneous syndromes among others.   Cardiomyopathy exome panel testing is the most cost-efficient and precise approach to diagnostic testing as there is overlap between phenotypes and the lack of characteristic “other” features in many instances.   Study of the panel genes from the DNA of a single individual allows us to focus on variants reported as pathogenic in the past, on those with a very low population frequency, with nucleotide conservation across species and with likely pathogenic consequence. When variants of unknown significance are identified by panel testing, DNA is requested from first degree relatives to interrogate the significance of the variant. There is no charge for added studies used to aid in interpretation of a sequence change found in the index case.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.   The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

Cardiac Arrhythmia Panel

Posted on by Melanie Pepin

Cardiac Arrhythmia exome panel testing includes more than 50 genes that have been identified to be responsible for disorders in which arrhythmia is a noted feature:

Cardiac Arrhythmia Panel Gene List

The disease phenotypes include Brugada syndrome, Familial atrial fibrillation, long QT, and arrhythmogenic right ventricular dysplasia among others.   Cardiac Arrhythmia exome panel testing is the most cost-efficient and precise approach to diagnostic testing as there is overlap between phenotypes and the lack of characteristic “other” features in many instances.   Study of the panel genes from the DNA of a single individual allows us to focus on variants reported as pathogenic in the past, on those with a very low population frequency, with nucleotide conservation across species and with likely pathogenic consequence. When variants of unknown significance are identified by panel testing, DNA is requested from first degree relatives to interrogate the significance of the variant. There is no charge for added studies used to aid in interpretation of a sequence change found in the index case.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.   The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

Testing for Known Pathogenic Variant

Posted on by Melanie Pepin

The Northwest Clinical Genomics Laboratory (NCGL) offers targeted analysis for variants previously identified in our laboratory.  Known pathogenic variant testing should be selected if such a variant was previously identified in the family by the NCGL (we tested a relative of the patient) and we have a positive control for that patient.

Panel on Demand

Posted on by Stephen Schildbach

For the patient with a rare phenotype, when the constellation of clinical findings is not recognized as part of a known syndrome, yet the clinician investigator would like to investigate a particular set of genes that are known to contribute to a particular phenotype, “panel on demand” sequencing is a cost-efficient and precise approach to diagnostic testing for rare inherited disease. Examples of panels might include a neurodevelopmental gene panel, hereditary cancer panel, cardiomyopathy gene panel or others. Study of the custom panel of genes from the DNA of a single individual is used to identify sequence variants with a very low population frequency, with nucleotide conservation across species and likely pathogenic consequence. Testing of a family trio facilitates filtering of sequence variants and reduces the number of potential candidates by looking for the same sequence alteration in an unaffected parent(s).

The NCGL offers several options for Panel on Demand based on the number of genes in the Panel:

  • Hyper Panel on Demand (201-500 genes)
  • Super Panel on Demand (101-200 genes)
  • Mega Panel on Demand (11-100 genes)
  • Micro Panel on Demand (2-10 genes)
  • Single Gene Sequencing

Use the web tool at https://ncgl.uwcpdx.org/panel-on-demand/ to add genes to create a custom panel.

See CPT Codes and Cost below for information on pricing.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.   The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

Exome Sequencing Re-analysis

Posted on by Stephen Schildbach

For the patient with a rare phenotype in whom exome sequencing did not identify a pathogenic variant in the past, re-evaluation of the original NCGL exome sequence data is offered when significant technological advances in sequencing technology and interpretation tools has occurred.  The clinician is encouraged to contact the NCGL laboratory director to request comparison of the technology at the time of earlier testing relative to the present.   Review of stored exome sequence files may be the most cost effective way of repeating examination of individual exomes.  Study of the exome from the DNA of a single individual is used to identify sequence variants with a very low population frequency, with nucleotide conservation across species and likely pathogenic consequence. Testing of a family trio facilitates filtering of sequence variants and reduces the number of potential candidates by looking for the same sequence alteration in an unaffected parent(s).

Exome Sequencing

Posted on by Stephen Schildbach

EXOME SEQUENCING of a single individual:  For the PROBAND with a rare phenotype, when the constellation of clinical findings is not recognized as part of a known syndrome, exome sequencing is the most cost-efficient and precise approach to diagnostic testing for rare inherited disease.   Study of the exome from the DNA of a single individual is used to identify sequence variants with a very low population frequency, with nucleotide conservation across species and likely pathogenic consequence.

EXOME SEQUENCING TRIO:    TRIO Exome sequencing is sequencing the entire exome of a proband and his/her parents. (as exome comparators)   TRIO testing allows filtering of rare sequence variants and reduces the number of potential candidates by looking for the same sequence alteration in unaffected parent(s).  The proband and parents may request reporting of rare sequence variants of medically actionable genes.*

EXOME SEQUENCING COMPARATOR:    Comparator exome sequence is an adjunct to exome sequencing of the proband; usually the parents are comparators.  Although individual rare variants are not reported for the comparator exome, using it only for comparison with the proband, the parent may request reporting of rare variants of genes known to be associated with adult disease for which medical action could alter outcome.*

*The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 59 genes associated with medically actionable conditions.  (Kalia, SS et al  Genetics in Medicine Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics  (17 Nov 2016)