During our more than 10 years dedicated to the field of genetic diagnosis of cardiovascular diseases, we have developed a knowledge management model that relies on a unique database able to integrate clinical infor-mation of the studied individuals, as well as molecular biology data from scientific publications and research groups we collaborate with, currently containing infor-mation from over 130 000 indivi-duals.
This database is essential for the development of patient-oriented medicine, allowing us to generate detailed reports with all the available clinical information about the detected variants. The quality and relevance of this information are assessed by experts at our laboratory who give advice on practical applications and recommendations for the clinical management of each patient.
KNOWLEDGE MANAGEMENT
MULTIDISCIPLINARYTEAM
We are a team of medical specia-lists in the field of neurology, clinical geneticists, biologists, cardiolo-gists, pharmacists, documentalists, nurses, epidemiologists, and bioin-formaticians, among others.
The development of neuroHIC services is complemented by close collaboration of the company with different research groups, as well as by our international network of experts who act as scientific advisors.
This allows us to offer top quality services based on the most complete and updated knowledge.
Our laboratory is equipped with the latest technology for massive DNA sequencing (NGS).The company has made a great effort to automate key laboratory processes (both in terms of equipment and software) in order to guarantee their traceability and minimize the probability of human errors, in compliance with the requirements of UNE-EN ISO 15189 as the highest quality standard for clinical laboratories.We are members of the European Molecular Genetics Quality Network (EMQN, UK), and we parti-cipate periodically in their external quality assessment (EQA) and comparative testing, both technical and interpretational, for neurological disorders.
CUTTING-EDGETECHNOLOGY
neuroHiC arises with the aim of providing analysis and interpretation of neurological disorders with a genetic basis as part of the services offered by Health in Code.Health in Code specializes in the diagnosis of inherited diseases that focuses on clinical practice and patient-oriented medicine.We are a technology-based company with headquarters in A Coruña and with an international scope, born after years of clinical experience and worldwide scientific collaborations.
We have a unique database model that is able to integrate clinical and molecular information from thousands of individuals
3
OUR CLINICAL REPORT
WIDE PORTFOLIO OF NGS PANELS
We have created a series of specific services aimed at enabling the molecular diagnosis of genetic neurological disorders through the implementation of the latest NGS technologies in combination with other more traditional molecular techniques (Sanger, MLPA, nucleotide repeat expansion analysis).Therefore we have designed a series of panels, both general and specific, with the purpose of serving as tools to support diagnosis in the clinical practice.neuroHiC panels include a comprehensive selection of genes described in clinical practice guidelines, as well as those that have been associated with disease in recent literature.These panels allow analyzing the main genes involved in each group of diseases in a single study (more than 630 related genes are included).
neuroHiC provides physicians with the necessary tools and information to make the best decisions based on the available information about each variant detected in the patient. The report is not intended to substitute for evaluation by a physician.The main aim is to guarantee the correct interpretation of the results, a fundamental tool to provide appropriate genetic counseling.neuroHiC offers the possibility to provide interpretation services for studies sequenced by our clients.
STUDYOF CNVs
To detect large duplications and deletions (CNVs), we have developed an algorithm based on comparative analysis of coverage data generated by our NGS studies.This approach allows us to maximize the diagnostic yield of our panels without increasing their cost.
PERSONALIZED COUNSELING:Our experts can offer support regarding study indication and interpretation of findings through direct and personal contact with our client.
The broad range of muscular disorders has greatly expanded in the last decades thanks to advances in the field of genetics. Although there are acquired causes of muscle disease (immunologic, toxic, endocrine-metabolic), genetic causes account for 80% of cases, with more than 200 known genes so far.As a whole, they are considered rare diseases, with an overall prevalence of 1/3 500 live births. The increase in survival and the discovery of new therapeutic targets have contributed to the growing importance of this group of pathologies. It is worth noting that, although they are chronic and usually progressive degenerative diseases, over 50% have their onset in childhood.The GMD comprehensive panel constitutes a global approach to the most relevant genes related to genetic muscle disorders, namely: structural and metabolic myopathies, congenital myasthenic syndromes, myotonia, and arthrogryposis.
Structural myopathies
The group of congenital structural genetic muscle disorders includes all genes related to congenital myopathy and congenital muscular dystrophy.Congenital myopathies comprise a group of disorders characterized by non-dystrophic morphological abnorma-lities on muscular biopsy. An approximate prevalence of 3.5-5/10 000 live births has been estimated (Sharma et al., 2009). Most of these diseases manifest at birth or shortly thereafter with hypotonia, delay in motor development, and static or non-progressive weakness. Although these symptoms may be present since birth, diagnosis is often not reached until well into childhood or even in adulthood, since many of these signs may go unnoticed.On the other hand, congenital muscular dystrophies, despite showing symptoms from birth, usually have a more severe and progressive development and are characterized by the presence of muscular dystrophy on biopsy.
We use the term "structural" for those forms of muscle disease that primarily affect the structure of muscle fibers and lead to alterations in their function.
To better assess this group of disorders, two main categories were considered based on the age of onset of symptoms:
• Congenital structural genetic muscle disorders (present from birth)• Child- and adult-onset structural genetic muscle disorders
For a general approach to structural genetic muscle disorders, including congenital, child- and adult-onset forms, a comprehensive panel of 107 related genes has been developed.
*LARGE1 (LARGE); SELENON (SEPN1) I The most relevant genes are highlighted in bold
*LARGE1 (LARGE); SELENON (SEPN1) I The most relevant genes are highlighted in bold
dystrophy, other forms of congenital muscular dystrophy with / without CNS involvement)• Rigid spine syndrome with respiratory failure
The group of child- and adult-onset structural genetic muscle disorders encompasses the rest of muscular dystrophies: a group of inherited diseases that affect skeletal muscle, characterized by a progressive degeneration of muscle fibers determining loss of strength. This heterogeneous group of diseases has been a subject of clinical and molecular studies for decades, leading to increasingly complex classifications based on genotype-phenotype correlation attempts.So far, one of the most useful classifications for the clinical practice is still the prevailing weakness pattern, which allows identifying phenotypes to guide genetic studies. We have relied on this classification to guide clinical decision making aimed at selecting the most suitable panel for molecular diagnosis:
• Dystrophinopathies (DMD)• Limb-girdle muscular dystrophies (both at the pelvic and shoulder level)• Emery-Dreifuss muscular dystrophy (characterized by a scapulohumeral-peroneal distribution and early
contractures, associated with heart disease)• Distal myopathies (with a pattern of weakness predominantly involving distal muscles)• Oculopharyngeal muscular dystrophy*• Facioscapulohumeral muscular dystrophy**
With the exception of oculopharyngeal muscular dystrophy*, whose main pathogenic mechanism is a triplet repeat expansion in the PABPN1 gene (analyzed in our laboratory on specific request), and facioscapulohumeral muscular dystrophy**, whose main pathogenic mechanism is the contraction of a repetitive region in the DUX4 gene (detected by a technique not performed in our laboratory), there are specific panels for the study of the remaining pathologies. We have developed an additional panel for the study of myofibrillar myopathies, selected for their characteristic findings on muscle biopsy.
Child- and adult-onset structural genetic muscle disorders panel
ADSSL1 ANO5 BAG3 BVES CAPN3 CAV3 CRYAB
DES DMD DNAJB6 DNM2 DYSF EMD FHL1
FKRP FKTN FLNC GNE HNRNPDL ISPD KLHL9
LAMP2 LDB3 LIMS2 LMNA MATR3 MYH2 MYH7
MYOT NEB PABPN1 PLEC POMGNT1 POMT1 POMT2
SELENON* SGCA SGCB SGCD SGCG SYNE1 SYNE2
TCAP TIA1 TMEM43 TNPO3 TOR1AIP1 TRAPPC11 TRIM32
TRIM54 TRIM63 TRPV4 TTN VCP VMA21 XK
[56 genes]
*SELENON (SEPN1) I The most relevant genes are highlighted in bold
Related phenotypes:• Duchenne muscular dystrophy• Becker muscular dystrophy• X-linked dilated cardiomyopathy• Other DMD-related phenotypes
Dystrophinopathies genetic study [DMD]For DMD, the following techniques can be performed:
• MLPA (for the detection of deletions/duplications of one or more exons) • NGS (able to detect CNVs, point mutations and small in/dels)
Oculopharyngeal muscular dystrophy study [PABPN1]Triplet repeat expansion analysis.
1. Darras BT, Menache-Stroninki CC, Hinton V, Kunkel LM. Neuromuscular Disorders of Infancy, Childhood and Adolescence: A Clinician’s Approach, 2nd ed, Darras BT, Jones HR Jr, Ryan MM, De Vivo DC (Eds), Academic Press, San Diego 2015.
Metabolic myopathiesMetabolic myopathies are a group of inherited muscular disorders secondary to enzymatic defects affecting metabolism and energy production in muscle. Some of them are considered inherited metabolic diseases and, although they are rare causes of myopathy, their diagnostic relevance lies in the fact that some of them are potentially treatable. Their symptomatology can mimic other forms of muscular dystrophy or inflammatory myopathies, and they often manifest with subtle symptoms such as asymptomatic CK elevation, muscle cramps, myalgia, or myoglobinuria. Their prevalence is unknown: Pompe disease (acid maltase deficiency) affects 1/40 000 people, and McArdle disease 1/100 000 people.Its etiopathogenesis is related to problems in the metabolism of glycogen, lipids or in mitochondrial oxidative phosphorylation. Therefore, we have designed three specific panels for each metabolic pathway and a comprehensive panel that includes the most relevant genes involved in this type of diseases.
AGL ENO3 GAA
GBE1 GYG1 GYS1
KLHL24 LAMP2 LDHA
PFKMPGAM2 PGK1
PGM1 PHKA1 PHKA2
PHKB PHKG2 PYGM
RBCK1
Glycogen storage myopathies panel
RELATED PHENOTYPES:GAA Pompe disease (type II glycogenosis)
PYGM McArdle disease (type V glycogenosis)LAMP2 Danon disease
PFKM Muscle phosphofructokinase deficiency (type VII glycogenosis)GYG1 / RBCK1 Polyglucosan body myopathy
MyotoniaMyotonia refers to a neurological symptom that describes difficulty in muscle relaxation after contraction. There may be an involvement pattern, although any muscle group can be affected.
Among hereditary myotonias, there are mainly two groups:
• Dystrophic myotonia (or myotonic dystrophy, whose main form is also known as DM1 or Steinert disease): Its prevalence is estimated to be about 1/8 000 individuals. Clinically, it is a multisystem disease where myotonia is accompanied by muscle weakness, cardiac conduction problems, cataracts, and endocrine and gastrointes-tinal alterations. Its molecular mechanism consists of a trinucleotide expansion in the DMPK gene; therefore, its diagnosis requires a specific test.
• Non-dystrophic myotonias belong to the group of channelopathies, and their genetic defect determines the occurrence of symptoms including myotonia as well as weakness, myalgias, episodes of paralysis, etc.
Congenital myasthenic syndromesCongenital myasthenia is a group of disorders caused by a biochemical defect or a structural alteration of the neuromuscular junction that leads to a clinical picture of muscle weakness and fatigability from birth or early infancy. It is important to distinguish these forms of the disease from myasthenia gravis (a disorder of autoimmune origin) and neonatal myasthenia (in children of mothers with myasthenia gravis).The prevalence of congenital myasthenic syndromes has been estimated between 1/500 000 (GeneReviews) and 9.2/1 000 000 (Parr et al., 2014). Its etiology is largely genetic. As of today, several involved genes are known, allowing for two thirds of cases to have a positive genetic diagnosis (Jacob et al., 2009).The most frequently involved genes and their diagnostic yields are CHRNE (50%), RAPSN (15-20%), COLQ (10-15%), DOK7 (10-15%), CHAT (5%), and GFPT1 (2%). The core panel includes these six genes, and we have also developed a comprehensive panel with 23 related genes that will allow optimizing the diagnostic yield.
1. Abicht A, Müller J S, Lochmüller H. Congenital Myasthenic Syndromes. 2003 May 9 [updated 2016 Jul 14]. In: Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJH, Bird TD, Ledbetter N, Mefford HC, Smith RJH, Stephens K, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2017.
2. Jacob S, Viegas S, Lashley D, Hilton-Jones D. Myasthenia gravis and other neuromuscular junction disorders. Pract Neurol. 2009 Dec;9(6):364-71.
3. Parr JR, Andrew MJ, Finnis M, Beeson D, Vincent A, Jayawant S. How common is childhood myasthenia? The UK incidence and prevalence of autoimmune and congenital myasthenia. Arch Dis Child. 2014 Jun;99(6):539-42.
REFERENCES
[23 genes]
[6 genes]
The most relevant genes are highlighted in bold
ArthrogryposisArthrogryposis, or arthrogryposis multiplex congenita (AMC), is characterized by the presence of non-progressive multiple joint contractures in different areas of the body present from birth. It is estimated that up to 1% of newborns are born with some type of congenital contracture, although the prevalence of arthrogryposis is estimated in 1/3 000 live births (Lowry et al., 2010). Approximately two thirds of affected individuals can be diagnosed by the age of two, and great progress is being made in the identification of specific genetic and non-genetic causes of arthrogryposis (Hall et al., 2014). It has been estimated that a genetic cause can be identified in approximately 30% of cases (Dimitraki et al., 2011).There are different forms that should be considered when selecting the genetic study:
• Amyoplasia or "classic arthrogryposis" accounts for one third of cases, with a prevalence of 1/10 000 live births. They are sporadic cases with all four limbs affected, unaffected trunk, and no multisystem involvement. They usually do not have a genetic cause, and their etiology is due to maternal-fetal factors in pregnancy. However, some forms can clinically resemble distal forms of arthrogryposis. Therefore, prior to a genetic study request, cases must be carefully selected based on clinical suspicion and potential differential diagnoses.
• Those individuals with associated CNS involvement (malformations, intellectual disability, or other developmental disorders) or dysmorphic features require an assessment involving chromosomal and gene dosage studies (karyotype, SNP-arrays, etc.).
• Targeted genetic studies are more adequate and have a higher yield for distal arthrogryposis and multiple pterygium-associated conditions, for which we have developed specific panels.
• It is worth noting that up to 5% of arthrogryposis cases are secondary to myopathies and congenital myasthenic syndromes (Darras et al., 2015), which are targeted by the arthrogryposis comprehensive panel.
Multiple pterygium syndrome, Escobar variant and related disorders panel
ECEL1 FBN2
MYBPC1 MYH2
MYH3 MYH8
PIEZO2 TNNI2
TNNT3 TPM2
Distal arthrogryposis panel
1. Dimitraki M, Tsikouras P, Bouchlariotou S, Dafopoulos A, Konstantou E, Liberis V. Prenatal assessment of arthrogryposis. A review of the literature. J Matern Fetal Neonatal Med. 2011 Jan;24(1):32-6.
2. Hall JG. Arthrogryposis (multiple congenital contractures): diagnostic approach to etiology, classification, genetics, and general principles. Eur J Med Genet. 2014 Aug;57(8):464-72.
3. Lowry RB, Sibbald B, Bedard T, Hall JG. Prevalence of multiple congenital contractures including arthrogryposis multiplex congenita in Alberta, Canada, and a strategy for classification and coding. Birth Defects Res A Clin Mol Teratol. 2010 Dec;88(12):1057-61.
4. Darras BT, Menache-Stroninki CC, Hinton V, Kunkel LM. Neuromuscular Disorders of Infancy, Childhood and Adolescence: A Clinician’s Approach, 2nd ed, Darras BT, Jones HR Jr, Ryan MM, De Vivo DC (Eds), Academic Press, San Diego 2015.
PMP22 Charcot-Marie-Tooth type 1A (CMT1A or duplication of the 17p12 region)PMP22 Tomacular neuropathy / hereditary neuropathy with liability to pressure palsies
(HNPP or deletion of the 17p12 region)GAN Giant axonal neuropathy
Charcot-Marie-Tooth (CMT) disease or hereditary motor and sensory neuropathy is the most frequent inherited neuromuscular disease, with a prevalence of 1/2 500 individuals (Suter and Sherer, 2003).CMT is a complex disorder at the molecular level, with at least 1 000 genetic variants associated with about 80 genes (Timmerman et al., 2014). In the wide series described, molecular alteration is identified in 60%-70% of patients (80% of demyelinating forms and 25% of axonal forms) (Rossor et al., 2015). Approximately 90% of alterations are found in genes PMP22, MPZ, GJB1, and MFN2 (DiVicenzo et al., 2015), although this number varies among populations and is particularly reduced in regions with a high prevalence of recessive inheritance forms. 40%-50% of CMT cases are type 1 (CMT1, demyelinating form), of which 70-80% are caused by a duplication of a region of about 1.5 Mb in 17p12 containing the PMP22 gene (CMT1A).Hereditary motor neuropathy (HMN) comprises 10% of all hereditary neuropathies, with a diagnosis rate of 20%-32% (Bansagi et al., 2017).
SOX10 Demyelinating neuropathy, central demyelination, Waardenburg / Hirschsprung disease
TTR Amyloid neuropathy
1. Bansagi B, Griffin H, Whittaker RG, Antoniadi T, Evangelista T, Miller J, Greenslade M, Forester N, Duff J, Bradshaw A, Kleinle S, Boczonadi V, Steele H, Ramesh V, Franko E, Pyle A, Lochmüller H, Chinnery PF, Horvath R. Genetic heterogeneity of motor neuropa-thies. Neurology. 2017 Mar 28;88(13):1226-1234.
2. DiVincenzo C, Elzinga CD, Medeiros AC, Karbassi I, Jones JR, Evans MC, Braastad CD, Bishop CM, Jaremko M, Wang Z, Liaquat K, Hoffman CA, York MD, Batish SD, Lupski JR, Higgins JJ. The allelic spectrum of Charcot-Marie-Tooth disease in over 17,000 indivi-duals with neuropathy. Mol Genet Genomic Med. 2014 Nov;2(6):522-9.
3. Rossor AM, Evans MR, Reilly MM. A practical approach to the genetic neuropathies. Pract Neurol. 2015 Jun;15(3):187-98. 4. Suter U, Scherer SS. Disease mechanisms in inherited neuropathies. Nat Rev Neurosci. 2003 Sep;4(9):714-26. 5. Timmerman V, Strickland AV, Züchner S. Genetics of Charcot-Marie-Tooth (CMT) Disease within the Frame of the Human Genome
Project Success. Genes (Basel). 2014 Jan 22;5(1):13-32.
REFERENCES
[22 genes]
[18 genes]
Sensory and autonomic neuropathy
Metabolic neuropathy
*ELP1(IKBKAP); RETREG1(FAM134B) I The most relevant genes are highlighted in bold
Movement disorders comprehensive panel [123 genes]
*PRKN(PARK2); PARK7(DJ1)
In addition to encompassing all the genes present in the different specific panels, some other genes belonging to rarer clinical pictures and with more complex phenotypes have been included. Among the ones covered by this panel, it is worth highlighting:
Dystonia is characterized by sustained or intermittent muscular contractions that lead to abnormal postures and movements, often repetitive. Symptoms of dystonia may appear from early childhood to late adulthood, affecting one (focal), several (multifocal, segmental), or numerous parts of the body (generalized). Generalized dystonia usually includes adolescent-onset progressive and incapacitating disorders with a known genetic basis. The group of primary focal dystonia generally appears in adults and usually involves the neck, face, or arms; the number of known genes is lower, although up to 25% of cases tend to have a positive family history (Steeves et al., 2012). It is worth noting that dystonias are diseases with great phenotypic and genotypic heterogeneity, often with incomplete penetrance even within the same family (Albanese et al., 2013).A prevalence of approximately 16/100 000 individuals is estimated (Steeves et al., 2012).Although numerous risk factors have been described by association studies, the diagnostic-genetic approach is aimed at performing diagnoses with a clinical application for the patient.For this, four phenotype groups have been established:
• Primary dystonia (isolated, focal, or generalized, as the main symptom): 8-gene core panel, with the particularly relevant genes TOR1A (DYT1), THAP1 (DYT6), and GNAL (DYT25, adult-onset craniocervical dystonia).
• Dopa-responsive dystonia (Segawa syndrome): 3-gene specific panel (GCH1, TH, and SPR).• Myoclonus-dystonia: 3-gene specific panel (SGCE [DYT11], whose yield is up to 50% in familial cases, and
TOR1A or [DYT1] and KCTD17, which are included as differential diagnoses).• Combined dystonia — dystonia-plus — or complex dystonia phenotypes: 24-gene extended panel for a more
comprehensive etiologic approach and for complex cases.
ANO3 ATP1A3 CACNA1B
CIZ1 COL6A3 GCH1
GNAL HPCA KCTD17
KMT2BMECR PNKD
PRKRA PRRT2 SGCE
SLC2A1 SLC30A10 SLC39A14
SLC6A3SPRTH
THAP1 TOR1A TUBB4A
Dystonia comprehensive panel
1. Albanese A, Bhatia K, Bressman SB, Delong MR, Fahn S, Fung VS, Hallett M, Jankovic J, Jinnah HA, Klein C, Lang AE, Mink JW, Teller JK. Phenomenology and classification of dystonia: a consensus update. Mov Disord. 2013 Jun 15;28(7):863-73.
2. Steeves TD, Day L, Dykeman J, Jette N, Pringsheim T. The prevalence of primary dystonia: a systematic review and meta-analysis. Mov Disord. 2012 Dec;27(14):1789-96.
Parkinsonism is a group of neurological diseases with symptoms including bradykinesia, muscle stiffness, resting tremor, and postural instability. Parkinson's disease, the most common form of parkinsonism and the second most frequent neurodegenerative disease (after Alzheimer's disease), is clinically characterized by these four cardinal motor symptoms, as well as by a good response to treatment with levodopa.Its prevalence is estimated to be between 1%-2% of the population at age 65 and about 4% at age 85. Approximately 15% of cases are familial, although some studies suggest that up to 60% of sporadic cases could be explained by genetic factors (Hamza et al., 2010). It is currently considered a multifactorial disease, with numerous environmental and genetic factors involved. The most commonly involved monogenic determinants have been selected for a core study panel for this disease, including SNCA, LRRK2, and VPS35 (with autosomal dominant transmission and generally late onset), and PRKN (PARK2), PINK1, and PARK7 (DJ1) (with autosomal recessive transmission and an earlier onset).For the study of early-onset parkinsonism, usually appearing during adolescence (<20 years), we have developed a specific panel with the most common causative genes.Other types of atypical parkinsonism and Parkinson-plus disorders (such as progressive supranuclear palsy, corticobasal degeneration, multiple system atrophy, or Lewy body dementia) are covered by the comprehensive panel.
ATP13A2 ATP6AP2
DCTN1 DNAJC6
FBXO7 GBA
LRRK2 MAPT
PARK7* PINK1
PLA2G6PRKN*
SNCA SYNJ1
VPS35
Parkinson and related disorders comprehensive panel
1. Hamza TH, Payami H. The heritability of risk and age at onset of Parkinson's disease after accounting for known genetic risk factors. J Hum Genet. 2010 Apr;55(4):241-3.
REFERENCES
Parkinson
GBA LRRK2 PARK7* PINK1 PRKN* SNCA VPS35
Parkinson's disease panel
ATP13A2 ATP6AP2 DNAJC6 FBXO7 PLA2G6 SYNJ1
Young-onset Parkinson's disease panel
[15 genes]
[7 genes]
[6 genes]
*PARK7 (DJ1); PRKN (PARK2) I The most relevant genes are highlighted in bold
*PARK7 (DJ1); PRKN (PARK2) I The most relevant genes are highlighted in bold
The most relevant genes are highlighted in bold
Although Huntington's disease is the most common form of chorea, it is estimated that 1%-7% of suspected cases have a negative HTT triplet expansion study (Martino et al., 2012), and other differential diagnoses must be considered. In addition to other non-genetic conditions (infectious, immune, toxic, or vascular), there are several phenocopies of Huntington's chorea that must be taken into account, for which this panel has been designed.
ATP7B C19orf12 CP
DCAF17FTL HPRT1
NKX2-1 NUP62 PANK2
PDE10APDE8B PDGFRB
PLA2G6 PRNP RNF216
SLC20A2 VAC14 VPS13A
XK
Chorea and Huntington-like disorders panel
1. Martino D, Stamelou M, Bhatia KP. The differential diagnosis of Huntington's disease-like syndromes: 'red flags' for the clinician. J Neurol Neurosurg Psychiatry. 2013 Jun;84(6):650-6.
Basal ganglia calcification is a nonspecific finding that can occur in the context of certain infectious, metabolic, and genetic syndromes. It can simply constitute a benign incidental finding (around 1% of CT scans performed for other reasons in patients over age 60), a sequel of a connatal infection. However, genetic study must be considered if clinical symptoms of unknown origin are present, particularly in patients with a positive family history.
Two conditions have been taken into account when developing this panel:• In children, Aicardi-Goutières syndrome (AGS) is an early-onset encephalopathy presenting with cerebral
atrophy, leukodystrophy, and typically basal ganglia calcifications and high interferon levels in CSF. Several related genes have been described (RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, TREX1, ADAR, and IFIH1), which reach a diagnostic yield of 90%-95% in cases with suspected AGS (Crow et al., 2015). Since its original description (Aicardi and Goutières, 1984), its phenotypic spectrum has been expanded, which must be taken into account particularly in late-onset forms.
• In adults in their third and fifth decades of life, idiopathic basal ganglia calcification (Fahr's disease) should be considered: it is an autosomal dominant condition, usually of familial presentation, characterized by the symmetrical calcification of basal ganglia and other regions of the brain. Its clinical picture can range from asymptomatic stages to a wide spectrum of neuropsychiatric symptoms. The genes involved so far are SLC20A2, XPR1, PDGFB, and PDGFRB.
1. Crow YJ, Chase DS, Lowenstein Schmidt J, Szynkiewicz M, Forte GM, Gornall HL, et al. Characterization of human disease pheno-types associated with mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, and IFIH1. Am J Med Genet A. 2015 Feb;167A(2):296-312.
REFERENCES
Basal ganglia calcification
ADAR IFIH1
PDGFB PDGFRB
RNASEH2A RNASEH2B
RNASEH2C SAMHD1
SLC20A2 TREX1
XPR1
Basal ganglia calcification comprehensive panel
ADAR IFIH1 RNASEH2A RNASEH2B RNASEH2C SAMHD1 TREX1
Aicardi-Goutières syndrome specific panel
[11 genes]
[7 genes]
The most relevant genes are highlighted in bold
The most relevant genes are highlighted in bold
NBIAS stands for ‘neurodegeneration with brain iron accumulation syndromes’ and covers a series of heterogeneous, often overlapping entities whose main characteristic is the accumulation of iron in the brain. This accumulation is predominantly observed at the level of basal ganglia on brain MRI (T2, spin-echo, and gradient echo sequences). One of its most frequent forms is pantothenate kinase-associated neurodegeneration (PKAN, formerly known as Hallervorden-Spatz syndrome), which is generally recognized on MRI by the "eye of the tiger" sign (a hypointense area with a hyperintense center in the globus pallidus).
The prevalence of these syndromes is estimated at around 1-3/1 000 000 individuals. They present clinically as neurodegenerative diseases with movement disorders and pyramidal, cerebellar, autonomic, and eventually cognitive and psychiatric signs.
Our NBIAS panel includes several causative genes, allowing for an approximate diagnostic yield of 65% (Schneider et al., 2016). In order of importance, it is worth highlighting the following genes: PANK2 (35%-50%), PLA2G6 (20%), C19orf12 (6%-10%), and WDR45 (1%-2%) (Gregory and Hayflick, 2014).
1. Gregory A, Hayflick S. Neurodegeneration with Brain Iron Accumulation Disorders Overview. 2013 Feb 28 [updated 2014 Apr 24]. In: Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJH, Bird TD, Ledbetter N, Mefford HC, Smith RJH, Stephens K, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2017.
REFERENCES
NBIAS (Neurodegeneration with brain iron accumulation syndromes)
ATP13A2 C19orf12
COASY CP
DCAF17 FA2H
FTL PANK2
PLA2G6 WDR45
Neurodegeneration with brain iron accumulation syndromes (NBIAS) [10 genes]
Paroxysmal movement disorders are a heterogeneous group of diseases with recurring episodes of symptoms related to involuntary movements characterized by a sudden onset and a more or less abrupt disappearance after a variable period. Strictly speaking, this definition includes several known forms of episodic dyskinesia, classified below according to their triggering factor.
• Paroxysmal kinesigenic dyskinesia (particularly associated with pathogenic variants in the PRRT2 gene)• Paroxysmal non-kinesigenic dyskinesia (particularly associated with pathogenic variants in PNKD and KCNMA1)• Exercise-induced dyskinesia (particularly associated with pathogenic variants in the SLC2A1 gene, also known
as glucose transporter deficiency or GLUT-1 deficiency).There are other clinical pictures that do not exactly constitute movement disorders, but they share the common characteristic of paroxysmal neurological symptoms with a fairly similar pathophysiological basis (many of them are channel-mediated) that, on occasion, can overlap to some degree in common clinical practice.
Inherited metabolic disorders are a group of diseases that include defects affecting enzymes or proteins involved in cellular metabolism. Many of these diseases have neurological manifestations and can present with complex clinical pictures, combining cognitive and muscular symptoms, ataxia, epilepsy, or movement disorders.Most commonly, movement disorders are not so much a predominant symptom as one of the manifestations of the disease. However, some metabolic disorders can start with some type of abnormal involuntary movement as their first symptom. Particularly, dystonia, myoclonus, chorea, stereotypies, and parkinsonism may be a part of this spectrum of manifestations. The importance of these diseases lies in the fact that many of them can be effectively treated and that their early identification can prevent neurological damage.In a cohort of patients with movement disorders studied by Gouider-Khouja et al. (2010), up to 29% were found to have a movement disorder secondary to metabolic disease, with dystonia and myoclonus as the most frequent symptoms (54% and 28%, respectively).
• One of the metabolic disease groups with the highest overall prevalence of movement disorders are mitochondrial diseases. Suspicion of any of these diseases should lead to the study of the mitochondrial genome or of nuclear genes involved in mitochondrial metabolism (see specific panel).
• On the other hand, we have selected some phenotypes that should be included in the differential clinical diagnosis due to the occurrence of a movement disorder as the first symptom:
1. Gouider-Khouja N, Kraoua I, Benrhouma H, Fraj N, Rouissi A. Movement disorders in neuro-metabolic diseases. Eur J Paediatr Neurol. 2010 Jul;14(4):304-7.
Hereditary spastic paraplegia has an estimated prevalence of 1.8/100 000. Genetic cause is identified in 33%-55% of families with autosomal dominant inheritance (AD-SP) and in 18%-29% of families with autosomal recessive inheritance (AR-SP). The most frequent form of AD-SP is SPG4 (SPAST), accounting for 40% of AD-SP forms and 20% of sporadic forms (Ruano et al., 2014). SPG3A (ATL1) is the cause of 10%-15% of AD-SP cases (up to 40% in SPG4-negative cohorts), with the most frequent form starting in the first decade of life (Giudice et al., 2014). SPG11 is the most common cause of AR-SP (20%-50%) (Stevanin et al., 2008).Anita Harding's historical description distinguishes pure and complicated forms (Harding, 1983). The pure form presents isolated pyramidal signs such as spasticity, hyperreflexia, Babinski sign, and motor deficits, which can be associated with sphincter disorder and deep sensitivity alterations. Complicated forms comprise several clinical entities combining spastic paraplegia with other neurological/non-neurological signs such as cerebellar ataxia, optic atrophy, retinitis pigmentosa, thinning of the corpus callosum, neuropathy, or epilepsy, among others.
*WASHC5 (KIAA0196) I En negrita, se señalan los genes más relevantes
1. Harding AE. Classification of the hereditary ataxias and paraplegias. Lancet. 1983 May 21;1(8334):1151-5. 2. Lo Giudice T, Lombardi F, Santorelli FM, Kawarai T, Orlacchio A. Hereditary spastic paraplegia: clinical-genetic characteristics and
evolving molecular mechanisms. Exp Neurol. 2014 Nov;261:518-39. 3. Ruano L, Melo C, Silva MC, Coutinho P. The global epidemiology of hereditary ataxia and spastic paraplegia: a systematic review of
prevalence studies. Neuroepidemiology. 2014;42(3):174-83. 4. Stevanin G, Azzedine H, Denora P, Boukhris A, Tazir M et al. SPATAX consortium. Mutations in SPG11 are frequent in autosomal recessive
spastic paraplegia with thin corpus callosum, cognitive decline and lower motor neuron degeneration. Brain. 2008 Mar;131(Pt 3):772-84.
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with a prevalence of 5.4/100 000 (Chiò et al., 2013). Although most cases are sporadic, 10% of patients have a positive family history. Pathogenic variants in genes C9orf72, SOD1, TARDBP, and FUS explain almost two thirds of the familial forms (>25%, 20%, 5%, and 5% respectively). Only one genetic alteration has been identified in the C9orf72 gene. It consists of a GGGGCC hexanucleotide expansion, which is not detectable by next-generation-sequencing.
Primary lateral sclerosis (PLS) is characterized by the isolated involvement of the upper motor neuron, which distinguishes it from amyotrophic lateral sclerosis, in which involvement of the lower motor neuron also occurs. The diagnosis of PLS is reached by excluding other causes of disease such as spastic paraplegia, multiple sclerosis, metabolic disease, or myelopathy.
1. Chiò A, Logroscino G, Traynor BJ, Collins J, Simeone JC, Goldstein LA, White LA. Global epidemiology of amyotrophic lateral sclerosis: a systematic review of the published literature. Neuroepidemiology. 2013;41(2):118-30.
REFERENCES
[28 genes]
The most relevant genes are highlighted in bold
RELATED PHENOTYPES:
ALS2, FIG4, SPG11, TBK1 Primary lateral sclerosis CHCHD10, SQSTM1, TBK1 Amyotrophic lateral sclerosis with / without frontotemporal dementia
SLC52A2, SLC52A3 Brown-Vialetto-Van Laere and Fazio-Londe syndrome
Dementia constitutes an important social, health, and economic problem. Twenty five percent of people over age 55 have a family history of dementia. In 2016, it affected 46.8 million people worldwide. With an exponential growth, this number is estimated to reach 131.5 million by 2050 (World Alzheimer Report 2016).Alzheimer's disease (AD) is the most common type of primary neurodegenerative dementia (60%-80% of cases). Approximately 25% of patients with AD have two or more affected relatives. Among familial forms, only 5% have an early onset (age <65 years). In these cases, transmission is autosomal dominant and is caused by pathogenic variants in genes PSEN1 (30%-70%), PSEN2 (<5%), and APP (10%-15%) (Loy et al., 2014). Allele 4 of the APOE gene represents a risk factor for AD (OR=2-3 in heterozygosis, OR=14.9 in homozygosis; Farrer et al., 1997), although the presence of the allele 4 of APOE is not necessary or sufficient to develop disease. Therefore, although genotyping of APOE can be clinically useful to support diagnosis in the context of other data suggesting AD, particularly in late-onset forms (age >65), its use is not indicated in asymptomatic individuals.Between 5% and 15% of pre-senile dementia cases (<65 years) are frontotemporal type, with a prevalence of 10-15/100 000 in the age group between 45 and 65 years. 25%-50% of patients with frontotemporal dementia have a family history of dementia or psychiatric disease, and 10%-30% are compatible with an autosomal dominant inheritance pattern (Rohrer et al., 2009). Pathogenic variants in C9orf72, GRN, and MAPT are involved in 80% of families with autosomal dominant forms. A single genetic alteration in the C9orf72 gene has been identified, consisting in a GGGGCC hexanucleotide expansion, not detectable by next-generation-sequencing.
1. World Alzheimer Report 2016; https://www.alz.co.uk/research/world-report-20162. Loy CT, Schofield PR, Turner AM, Kwok JB. Genetics of dementia. Lancet. 2014 Mar 1;383(9919):828-40. doi: 10.1016/S0140-
6736(13)60630-3. 3. Farrer LA, Cupples LA, Haines JL, Hyman B, Kukull WA, Mayeux R, Myers RH, Pericak-Vance MA, Risch N, van Duijn CM. Effects of
age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium. JAMA. 1997 Oct 22-29;278(16):1349-56.
4. Rohrer JD, Guerreiro R, Vandrovcova J, Uphill J, Reiman D, Beck J, Isaacs AM, Authier A, Ferrari R, Fox NC, Mackenzie IR, Warren JD, de Silva R, Holton J, Revesz T, Hardy J, Mead S, Rossor MN. The heritability and genetics of frontotemporal lobar degeneration. Neurology. 2009 Nov 3;73(18):1451-6.
Mitochondrial disorders are overall the most common group of inherited metabolic diseases, and they are among the most frequent hereditary neurological diseases.
They are clinically heterogeneous, can occur at any age, and generally manifest with a wide array of clinical symptoms, usually being defined as multisystem diseases. Some mitochondrial disorders can be grouped into specific syndromes such as Leigh syndrome (subacute necrotizing encephalomyelopathy), MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes), or Alpers-Huttenlocher syndrome. Diagnosis is usually based on clinical criteria, as well as on biochemical and histochemical analysis of biopsies. Genetic study contributes to the improved clinical and molecular characterization of these patients and allows providing adequate genetic advice for the individuals and their families.
The prevalence of childhood-onset mitochondrial diseases is 5-15/100 000 individuals (Gorman et al., 2014). The most common form of presentation is Leigh syndrome (2.5/100 000). The prevalence in adults is estimated in 9.6/100 000 (due to mtDNA mutations) and 2.9/100 000 (due to mutations in nuclear genes).
The mitochondrial defect can be caused by mutations in nuclear DNA (nDNA) or mitochondrial DNA (mtDNA) genes. With regard to genetic suspicion, it is worth noting that 80% of mitochondrial diseases in adults are due to pathogenic variants in mtDNA; however, these variants only account for 20%-25% of childhood-onset cases (in which nuclear genes have a greater importance) (Gorman et al., 2014).
We have developed a selection of specific panels for the study of mitochondrial diseases based on the main biochemical findings, as well as a core panel for the study of nuclear gene-encoded Leigh syndrome, with a comprehensive panel including 174 known genes for mitochondrial diseases.
1. Gorman GS, Chinnery PF, DiMauro S, Hirano M, Koga Y, McFarland R, Suomalainen A, Thorburn DR, Zeviani M, Turnbull DM. Mitochondrial diseases. Nat Rev Dis Primers. 2016 Oct 20;2:16080.
REFERENCES
[12 genes]
[11 genes]
*COQ8A (ADCK3); COQ8B (ADCK4); FDX2 (FDX1L)
RELATED PHENOTYPES:• Myoclonic epilepsy with ragged-red fibers (MERRF)• Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke (MELAS)• Leber hereditary optic neuropathy (LHON)• Neuropathy, ataxia, and retinitis pigmentosa (NARP)• Chronic progressive external ophthalmoplegia (CPEO)• Kearns-Sayre syndrome• Leigh syndrome• Pearson syndrome
Mitochondrial genomeAnalysis of the 37 mtDNA genes and their disease-associated variants. The detection of point mutations and large deletions, as well as the possibility to determine the degree of heteroplasmy in the submitted sample, are included in this study.
[37 genes]
• Friedreich’s ataxia [FXN]
Other nucleotide repeat expansions
Sample shipment
STUDY REQUISITION FORMThe sample for genetic testing must be sent together with a correctly filled requisition form (including clinical data and statement on the existence of informed consent).Available at www.neurohic.com or by request at [email protected]
SAMPLE COLLECTION
3 to 5 ml in EDTA tubes NGS > 5-10 μg (A260/280 = 1.8-1.9) Sanger > 1 μg (A260/280 = 1.8-1.9)
Please use the indicated kit for sample collection. You can request it at [email protected]
SAMPLE PACKAGING Each primary container (sample tube**) must be placed inside a secondary container (sealed plastic bag or Falcon tube) with enough absorbent material. Secondary recipients must be secured inside a rigid package or box with appropriate cushioning material.** Please make sure that the sample tube is labeled with the patient’s details or reference.
SAMPLE SHIPMENT Schedule your shipment so that sample reception takes place Monday to Thursday from 8:00 to 17:00.
We will deliver our report via:• Certified email• Health in Code Client Portal
RESULTS
HEALTH IN CODE S. L. Edificio O Fortín, As Xubias, s/n Campus de Oza 15006 A Coruña, Spain
Tel: +34 881 600 003If you wish, you can request a pick-up service at [email protected]
*For delivery in over 48 h, controlled-temperature shipment (4-8 ºC) is recommended
![ALK-TPM3 rearrangement in adult renal cell carcinoma: a case … · 2019. 10. 18. · carcinoma and, recently RCC [2–10]. Several groups had continuously reported translocation-associated](https://static.documents.pub/doc/80x56/60d4f7bf7877bd26fd2f137f/alk-tpm3-rearrangement-in-adult-renal-cell-carcinoma-a-case-2019-10-18-carcinoma.jpg)
