“singleton” sequencing.<\/strong><\/p>\nSingleton:<\/strong> This term refers herein to when only DNA from the patient is sequenced. While not
\nperfect, most of the advantages of sequencing can be gained from testing the patient alone, at
\nleast in many patients (see below).<\/p>\nTriome:<\/strong> This term refers to when DNA from the patientand both parentsare sequenced. Triome
\nsequencing offers certain advantages over singleton sequencing, including:<\/p>\n\n- The primary advantage of triome is the identification ofde novovariants, which are
\n“new mutations” that are present in the patient but absent in both parents. Triome
\nsequencing is frequently often used in patients with neurodevelopmental disorders
\n(intellectual disability, autism, etc.), epilepsy, “syndromes”, and\/or birth defects,
\nwhereasde novo variants are fairly common and oftentimes the main cause of the
\npatient’s disease.<\/li>\n - Most metabolic disorders are autosomal recessive, in which both parents are (usually
\nunaffected) carriers of one disease-causing variant each, and the patient inherited both
\nof these variants, resulting in disease. When two different variants that might be
\ndisease-related are identified in a patient, recessive disease is likely. To be disease
\ncausing, each variant should be on a different chromosome, inherited one each from
\nboth parents (in which the \u201cphase\u201d is termed as being “in trans”). The alternative is that
\nboth variants are located on the same chromosome, inherited from only one parent (in
\nwhich the \u201cphase\u201d is termed as being “in cis”). In the latter case, the variants are likely
\nnot disease causal, but could be a risk factor. The easiest, and often the only, way to
\ndetermine the phase of the variants (in cis versusin trans) is to sequence at least one
\nparent.<\/li>\n - In the case that one parent is clinically affected, sequencing can determine which of
\nseveral “variants of uncertain significance” were inherited from the affected parent.
\nObviously, these variants would be more important to consider than are the variants
\ninherited from the unaffected parent.<\/li>\n<\/ul>\nThe purpose of triome sequencing is to better understand the sequence results in the patient.
\nTriome sequencing is NOT intended to identify genetic disease or risks is the parents, most of
\nwhich will not be identified. Of course, triome sequencing will identify a parent as having a
\ndisease-causing variant if both the patient and a parent share the variant.
\nOf note, triome sequencing can be used for large panels, whole exome sequencing (WES),
\nand whole genome sequencing (WGS).<\/p>\n
As a practical matter, triome sequencing is recommended forpatients with neurodevelopmental
\ndisorders (intellectual disability, autism, etc.), epilepsy, “syndromes”, and\/or birth defects,
\nwhereas in many other settings, singleton sequencing is appropriate.[\/vc_column_text][\/vc_tta_section][vc_tta_section title=”One of my patients is interested in getting genetic testing done, but the father is unavailable. Is genetic testing still possible and useful?” tab_id=”1529705812703-0d602b4f-83f7″][vc_column_text]Before reading on, read the section entitled \u201cTriome versus singleton testing\u201d. Certainly, all
\nof the advantages of singleton testing are available if one parent is unavailable, or even if both
\nparent are unavailable (e.g. the child is adopted).
\nHowever, without both parents, de novo variants cannot be identified. If only one parent is
\navailable, sequencing of that parent can be helpful in terms of phasing if two variants of interest
\nin the same gene are found (see #2 in \u201cTriome versus singleton testing\u201d). Furthermore, the parent
\nof origin can generally be determined from a single parent (see #3), as a de novo variant is very
\nunlikely if the variant identified is not very rare.[\/vc_column_text][\/vc_tta_section][vc_tta_section title=”How do I choose the correct genetic test(s) for my patient?” tab_id=”1529705897129-1c574136-cddc”][vc_column_text]Choosing the correct test(s) is complicated, is based on the specifics of each available case,
\nand is best determined by a genetics professional or highly-knowledgeable physician. The
\ninformation herein is simplified into general principles in order to assist physicians to order the
\ncorrect testing in many less-complicated situations. To some degree, this is an opinion piece
\nwritten by Dr. Boles, although the opinions herein are shared by many geneticists. Before
\nreading on, please read the sections entitled \u201cThe different levels of genetic sequencing\u201d,
\n\u201cAdditional genetic testing to consider beyond nuclear sequencing\u201d, and \u201cTriome versus
\nsingleton testing\u201d.<\/p>\n
\n- Choose the appropriate level of sequencing:\n
\n- Lower levels of testing such as single variant sequencing, single gene sequencing,
\nand small sequencing panels are only indicated if the exact diagnosis is highly
\nsuspected, and an inexpensive test is desired for confirmation. If the test is
\nnegative, then testing should be reflexed to a higher level, generally WES.<\/li>\n - Large panels are appropriate for certain conditions, but are generally being
\nreplaced by WES as the difference in the costs narrows, especially considering the
\nadded price of reflux to WES should panel testing be negative or inconclusive.<\/p>\n\n- Note that all testing below the level of WES will become outdated very
\nrapidly as additional variants and genes are rapidly being associated with
\ndisease.<\/li>\n<\/ul>\n<\/li>\n - WES is the standard level of testing for most patients undergoing sequencing for
\nmetabolic, morphological (syndromes), neurological, and neurodevelopmental
\nconditions.<\/p>\n\n- WES has the most favorable current-clinically-relevant-information to
\ncost ratio among all levels of testing, baring cases in which the physician
\nis confirming a highly-suspected diagnosis or variant identified in a
\nrelative.<\/li>\n - Note that even WES will become outdated as additional non-
\nexonic variants are associated with disease.<\/li>\n<\/ul>\n<\/li>\n - WGS is of clinical relevance in cases whereas multiple testing is considered. In
\nparticular, WGS in some laboratories can provide all of the following testing, for
\none cost: whole genome (including WES), CMA, mtDNA sequencing, fragile X
\nand other trinucleotide repeats. In some cases, WGS is less expensive than
\nindividual testing.<\/li>\n<\/ul>\n<\/li>\n - Choose singleton or triome for sequencing:\n
\n- Triome testing is recommended for early-onset cases with neurodevelopmental
\ndisorders (intellectual disability, autism, etc.), epilepsy, and morphological
\nconditions (“syndromes”, birth defects).<\/li>\n - Singleton testing is recommended for most other conditions, including late-onset
\nneurological and functional disorders<\/li>\n<\/ul>\n<\/li>\n - Choose additional testing:\n
\n- CMA as appropriate, particularly in cases with congenital anomalies, intellectual
\ndisability, autism, and\/or epilepsy.<\/li>\n - mtDNA sequencing as appropriate, particularly in cases with multiple functional
\nsymptomatology, any neurological or neurodevelopmental condition, and\/or a
\nmultisystem condition.<\/li>\n - Trinucleotide repeat testing as appropriate, particularly fragile X testing in cases
\nwith intellectual disability or autism. Testing for other repeats should be
\nconditioned for ataxias or certain movement disorders.<\/li>\n - Imprinting\/methylation testing as appropriate, particularly Angelman syndrome
\ntesting in cases with intellectual disability, autism, and\/or epilepsy. Consider
\nPrader-Willi syndrome testing as appropriate, particularly in cases with overeating
\nand hypotonia.<\/li>\n<\/ul>\n<\/li>\n - Choose a laboratory, based on the following criteria:\n
\n- Testing: Does the laboratory do all of the testing requested. However, sometimes
\nit is appropriate to send testing to two or more laboratories.<\/li>\n - Methodology: Does the laboratory use best practices? Does it \u201cmiss\u201d diagnoses
\nfound elsewhere?<\/li>\n - Reporting: Does the laboratory report contain the information desired for a
\nclinical interpretation?<\/p>\n\n- Laboratory reporting vary tremendously in terms of the reporting of
\nvariants of uncertain significance, how narrow is considered \u201con target\u201d
\nversus \u201cincidental\u201d, and in regards to polygenic and integrative modeling.<\/li>\n<\/ul>\n<\/li>\n - Pricing: Certainly, lower is better. However, in determining price, remember to
\nconsider parental testing\/confirmation (e.g. triome pricing, does the laboratory
\nconfirm positive CMA variants for no extra charge), bundling (e.g. some labs
\ninclude mtDNA in WES\/WGS, most testing can be bundled in WGS), insurance
\ncoverage, and out-of-pocket pricing and liability for families (especially, will the
\nfamily receive an unexpected bill if insurance fails to pay?).<\/li>\n - Invasiveness: Blood, saliva, or buccal swabs?<\/li>\n
- Process: Does the laboratory provide assistance with ordering and insurance
\ncoverage? Is full sequence data transferred easily upon request? Are results sent
\npromptly? Are questions answered promptly and professionally?<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n[\/vc_column_text][\/vc_tta_section][vc_tta_section title=”When is it appropriate to order genetic testing when there is already a diagnosis that appears to explain the patient’s disease?” tab_id=”1529706226936-1750dc28-58d5″][vc_column_text]In many cases, a patient already has a diagnosis. This diagnosis may be based on a variety of
\ndifferent criteria. There are several situations in which additional genetic testing can be helpful
\nand is indicated:<\/p>\n
\n- The current diagnosis is only a description: Most patients carry a diagnosis that is simply
\na description of the patient\u2019s disease, and the diagnosis is not an underlying physiological
\nor genetic cause or factor. Examples include epilepsy, autism, intellectual disability,
\nmigraine, cyclic vomiting syndrome, chronic fatigue syndrome, fibromyalgia, and many
\nothers. In these cases, genetic testing is often indicated in order to identify underlying
\ndisease-related factors or causes, some of which may be treatable.<\/li>\n - The current diagnosis is in doubt: In many cases, the diagnosis is not definitive, and may
\nor may not be correct. In these cases, genetic testing is often indicated in order to look for
\nalternative potential diagnoses, some of which may be treatable.<\/li>\n - The primary diagnosis is likely correct, but does not account for all of the clinical
\nmanifestations present in the patient: In these cases, genetic testing is often indicated in
\norder to identify additional underlying disease-related factors or causes, some of which
\nmay be treatable. A common example is a patient who has a copy number variant (CNV)
\nidentified on chromosomal microarray (CMA) that fits the patient\u2019s phenotype, but was
\ninherited from a minimally affected or unaffected parent. Obviously, the CNV alone
\ncannot cause the patient\u2019s disease, and the CNV is assumed to be a risk factor, for which
\nadditional risk factors remain to be identified. Most patients with complex disease,
\nincluding all of the conditions listed in the first bullet above, are thought to have multiple
\nfactors, both genetic and environmental, that together lead to the development of disease.<\/li>\n - A phenotype is of significant distress to patient\/family, and is refractory to the usual
\ntherapies: Never assume that all of the factors leading to disease have been identified, as
\neven siblings with the same \u201cmonogenic\u201d disorder generally demonstrate wide
\nphenotypic heterogeneity. In treatment-refractory cases, genetic testing is often indicated
\nin order to identify additional underlying disease-related factors or causes, some of which
\nmay be treatable. An example is a patient with a known epilepsy-predisposition gene in
\nwhich seizure are severe and refractory despite standard and gene-specific therapies.<\/li>\n<\/ul>\n[\/vc_column_text][\/vc_tta_section][\/vc_tta_accordion][\/vc_column][\/vc_row]<\/p>\n","protected":false},"excerpt":{"rendered":"
[vc_row][vc_column][vc_column_text]This section is a work in progress. If you have a question that is not answered herein, ask us. If your question is brief and general (not regarding a specific patient or person), our Director (Richard G. Boles, M.D.) will provide a brief generalized response. If your question is thought to be of interest to […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-398","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/molecularmitomd.com\/index.php?rest_route=\/wp\/v2\/pages\/398","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/molecularmitomd.com\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/molecularmitomd.com\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/molecularmitomd.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/molecularmitomd.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=398"}],"version-history":[{"count":23,"href":"http:\/\/molecularmitomd.com\/index.php?rest_route=\/wp\/v2\/pages\/398\/revisions"}],"predecessor-version":[{"id":643,"href":"http:\/\/molecularmitomd.com\/index.php?rest_route=\/wp\/v2\/pages\/398\/revisions\/643"}],"wp:attachment":[{"href":"http:\/\/molecularmitomd.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=398"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}