Center for Personalized Medicine
About the Center for Personalized Medicine
Using personalized medicine, we predict that in the future:
- Diseases will be diagnosed earlier and more accurately
- Treatments will be safer and more effective
- Visits to the doctor will focus on prevention
- Conditions will be treated before symptoms ever emerge
- Health care costs will decrease due to early diagnoses, intervention and preventive medicine
The Division of Genomic Medicine’s Center for Personalized Medicine (CPM) is committed to using genetic information to enable pediatric personalized medicine at CHLA. Our testing is designed to create new ways for our clinical colleagues to detect, diagnose, treat and prevent childhood disease. We are committed to discovering the human genome’s potential to guide preventive medicine, targeted therapies and personalized health care for the benefit of generations to come.
The Center for Personalized Medicine works at the forefront of the genomic revolution by integrating state-of-the-art sequencing and other molecular technologies with cutting-edge bioinformatics and expert clinical and diagnostic professionals to develop innovative clinical testing for pediatric cancer, other complex conditions such as epilepsy, and inherited diseases.
The goals of the Center include using research and collaboration to:
- Unravel the genetic basis of disease and create treatment options based on genetic profiles that can be applied to subsets of patients and ultimately individual patients
- Lead genetics-based pediatric clinical trials
- Set new standards for using personalized medicine to effectively diagnose, treat and care for children
- Discover therapies— and even cures— for childhood diseases that currently have no effective treatment
Personalized Medicine Team
The Center is part of the Division of Genomic Medicine, Department of Pathology and Laboratory Medicine, and includes physicians, scientists, genetic counselors and staff who are internationally recognized for their expertise in genomics, clinical genetics, bioinformatics and molecular diagnostics.
Every day, these professionals work to realize the potential of personalized medicine at Children’s Hospital Los Angeles. The ability to provide complete genomic information for every child can be used to develop personalized, lifelong health plans. The research being conducted within the scope of personalized medicine at CHLA crosses divisions and disorders.
- Genetic Diseases
CHLA is at the forefront of discovering new genetically-driven cancer treatments. Led by internationally renowned pediatric hematologist-oncologist Alan S. Wayne, MD, the Cancer and Blood Disease Institute conducts innovative clinical trials and laboratory research to identify new therapies for children with acute lymphoblastic leukemia, neuroblastoma and brain tumors. The Institute is home to multiple phase I clinical trial consortia to test pioneering treatments for these diseases.
At The Vision Center, led by Thomas C. Lee, MD, physicians are researching the origins of retinoblastoma, the most common eye tumor in children, as well as developing new approaches to detect and treat this devastating disease.
Timothy Triche, MD, PhD, co-Director of CHLA’s Center for Personalized Medicine, is an internationally recognized leader in genomics and pediatric cancer. His research, in collaboration with the Division of Anatomic Pathology, has made CHLA one of the leading institutions worldwide for diagnosing and treating pediatric sarcomas.
There are a number of health conditions that have an especially high genetic risk factor, including craniofacial abnormalities, epilepsy, autism and heart defects. Working with world-class leaders, the Center for Personalized Medicine will use the latest genomic technologies to more accurately determine the genetic causes of these diseases, develop genomic-based tests to identify the diseases in pediatric patients—including early detection in newborns—and develop new treatments for patients who suffer from inherited diseases.
The CPM team is working with investigators in several clinically focused areas to develop comprehensive approaches for genetic testing, including the following:
The Division of Neurology at CHLA offers comprehensive services for children with epilepsy, neurofibromatosis, movement disorders, and muscular dystrophy, as well as a variety of neurogenetic, degenerative, and leukodystrophy disorders. The CPM will work in partnership with clinicians in Neurology to offer diagnostic genetic testing across a spectrum of disease areas.
Pat Levitt, PhD, the director of the Developmental Neurogenetics Program at the Institute for the Developing Mind at CHLA, is one of the leading authorities on the biological origins of autism and other neurodevelopmental disorders.
Clinical (Constitutional) Genetic Testing
Neonatal and pediatric patients with features of a recognizable or suspected genetic condition, or those who experience delays in development or intellectual disability, can benefit from our clinical genetic testing. The results of this testing can aid in diagnosis as well as support the development of specialized treatment plans. Our interdisciplinary team includes laboratory directors who are Board-certified in clinical cytogenetics and molecular genetics, bioinformaticians, clinical geneticists and genetic counselors to help guide physicians, patients and their families to better understand the testing process as well as the interpretation of test results. We are internationally recognized for our specialized expertise in pediatric oncology and offer a comprehensive range of tests for analysis of hematologic disorders, central nervous system tumors, and solid and soft tissue tumors.
- 22q11.2 Deletion/Duplication Analysis
- Chromosomal Microarray Analysis
- Clinical Exome Sequencing
- Epilepsy Gene Panel
- Ocular Disease Focused Exome
- Focused Exome
The Department of Pathology and Laboratory Medicine and Center for Personalized Medicine now offers 22q11.2 Deletion/Duplication Analysis by multiplex ligation-dependent probe amplification (MLPA). This test is indicated for individuals with a variety of disorders associated with copy number alterations of this region of chromosome 22q, including 22q11.2 Microdeletion syndrome (DiGeorge/Velocardiofacial syndrome), the reciprocal 22q11.2 duplication syndrome and Cat Eye syndrome (CES; partial tetrasomy of chromosome 22).
This assay is indicated for individuals who are suspected of having a 22q11.2 copy number variant based on clinical manifestations, which may include characteristic craniofacial features, congenital heart defect, cleft palate, learning difficulties, renal anomaly, and immune deficiency. For CES, these clinical features can include anal atresia, coloboma and cardiovascular malformations. This assay is also indicated for individuals who are known to have a cytogenetically-determined variant by karyotype or FISH studies, involving the 22q11.2 region, but need a more detailed characterization of the chromosomal breakpoints. There is a wide spectrum of phenotypic variability associated with individuals who carry a 22q11.2 copy number variant, even among affected family members. The assay is therefore also appropriate for individuals with a family history of a 22q11.2 deletion or duplication, even if the individual is not known to manifest the typical clinical features.
The 22q11.2 Deletion/Duplication Analysis by MLPA will allow for identification of a microdeletion or a microduplication in the 22q11.2 region. However, to specifically screen for low-level mosaicism of a chromosome 22 structural alteration, fluorescence in situ hybridization (FISH) analysis may be a more appropriate assay. Acceptable sample types include whole blood in an EDTA tube (purple top) and extracted DNA.
The American College of Medical Genetics (ACMG), the American Academy of Neurology (AAN), and the American Academy of Pediatrics (AAP) all recommend Chromosomal Microarray Analysis as the first tier diagnostic test for pediatric patients with multiple congenital anomalies, developmental delay, intellectual disability, and autism spectrum disorders.
Chromosomal Microarray Analysis provides a high-resolution genome-wide DNA copy number assessment. It also allows for the detection of Absence of Heterozygosity - AOH (also referred to as long continuous stretches of homozygosity), which in some cases may be indicative of Uniparental Disomy (UPD). Chromosomal Microarray Analysis is performed using the Affymetrix CytoScan HD Microarray to identify DNA copy number gains and losses associated with chromosomal imbalances.
Clinical exome sequencing (CES) is a highly complex test to identify changes among the ~20,000 genes that encode proteins that the body uses for its many processes. A critical genetic change may identify a cause for a medical condition. The collection of the entire set of genes is called the genome. The exons make up less than 2% of the genome but account for the vast majority of functional genetic mutations. “Exome” refers to the parts of the genome formed by all the exons. While traditional sequencing tests target one gene or a small group of related genes at one time, the CES test targets the whole exome simultaneously, providing an efficient and powerful clinical diagnostic tool for a variety of genetic disorders, particularly when a patient’s sample is analyzed together with those of both parents, as a trio. The intent of this test is to provide a genome-wide assessment that is cost-effective and substantially more efficient than multiple traditional sequential genetic testing methods. In some cases, a molecular diagnosis provides additional information about a medical condition that may modify the healthcare management and/or treatment an individual is currently receiving.
Genetic counseling prior to consenting to CES is recommended to fully understand the benefits, risks, and limitations of exome sequencing. Post-test genetic counseling should also be provided by a genetic counselor, physician, or other authorized healthcare provider to give information about clinically relevant results and available interventions or resources. Continued follow-up at a genetics clinic may be recommended. Additionally, a molecular diagnosis may be used for family planning purposes and to help identify family members who may be “at-risk” of developing a similar medical condition.
Additional Medically Actionable Results
Exome sequencing may identify a previously undiagnosed genetic condition that is not related to the symptoms for which the CES was initially ordered. This is considered an “incidental finding”. For example, a result may indicate that an individual has a hereditary predisposition to develop cancer or cardiomyopathy. The symptoms of these conditions may not be apparent at the time of testing and they may or may not occur in the future. These results are called medically actionable because a physician may modify an individual’s healthcare management based on these results. In 2013, the American College of Medical Genetics and Genomics (ACMG) released an updated guideline of genes to be reported as medically actionable, incidental findings. A list of these genes can be found on the ACMG website. Variants in these genes, or other reportable genes as indicated by recent clinical literature and publications, will be reported as incidental findings only if they are known to be disease causing or expected to be disease-causing. Variants of unknown significance will not be reported.
Epilepsy is a common neurological disorder that affects almost 1% of the general population. The etiology of childhood epilepsy is complex, and it is estimated that approximately 40% of affected individuals have a seizure disorder with an underlying genetic origin. In many cases, epilepsy is the only presenting feature, while in other patients epilepsy is part of a spectrum of complex clinical findings. Significant clinical overlap exists among the different genetic disorders associated with childhood epilepsy, and determination of the genetic cause in newly diagnosed patients can be challenging. However, identifying the molecular cause is important to confirm a clinical diagnosis, obtain prognostic information and to assist with decisions about treatment. In addition, knowledge of the exact genetic cause of epilepsy in the proband enables testing of other relatives at risk, increases the accuracy of recurrence risk counseling and allows prenatal diagnosis for known familial pathogenic variants.
New modalities for molecular genetic testing, including next-generation sequencing (NGS), enable efficient, simultaneous and cost-effective evaluation for mutations in multiple genes associated with epilepsy. The Center for Personalized Medicine, working closely with epilepsy experts from the Division of Neurology at CHLA, has developed a comprehensive NGS-based test for disease-causing mutations in more than 224 genes associated with seizure disorders in children.
Genetic factors play a role in several eye diseases. The inherited eye disease may be a part of a syndrome where other organs are also affected or it could be an isolated finding (non-syndromic).
The Ocular Disease Focused Exome test is indicated for individuals with isolated (non-syndromic) ocular phenotypes with a suspected genetic etiology and a clinical diagnosis of inherited retinal dystrophy, early-onset glaucoma or optic atrophy. There is a great deal of clinical and genetic heterogeneity in these diseases, and to date, more than 270 genes have been identified. The CPM Ocular Disease Focused Exome test has been developed using our Clinical Exome backbone. This provides a genome-wide assessment of all genes that is substantially more efficient than traditional sequential single gene testing, with the built-in flexibility to add newly discovered disease genes.
The CPM Ocular Disease Focused Exome test is currently used to interrogate the exons and canonical splice-sites of 270 nuclear genes, including 253 genes known to be associated with inherited retinal dystrophy, 22 genes known to be associated with early-onset glaucoma and optic atrophy, and 5 genes that are shared amongst the diagnostic categories. In addition, the assay includes complete mitochondrial DNA genome sequencing and mutation analysis. Due to technical limitations of exome sequencing, this assay does not cover CEP290 deep intronic mutations, mutations in the highly repetitive and challenging RPGR ORF15 exon, and exon level copy number alterations. For patients with a strong suspicion for pathogenic mutations in these regions based on clinical history, alternative testing may be recommended.
The etiologies of inherited retinal dystrophy, early-onset glaucoma and optic atrophy are complex, which translates to varying diagnostic rates for different types or subtypes of diseases. The overall sensitivity of genetic testing is, however, estimated to be above 50%.
The exact genetic diagnosis of these inherited diseases may assist in genetic counseling as well as clinical management of these patients using novel treatment approaches.
If the Ocular Disease Focused Exome test is non-informative, the clinical care provider may obtain consent for whole exome sequence analysis as an extension of the panel. No additional blood samples will be required. In contrast, whole exome sequencing should be considered for patients with more complex clinical presentations and multiple system involvement, not limited to eye disease.
Exome Sequencing is indicated for individuals suspected to have a disease associated with an underlying genetic disorder. This test covers the exonic (protein-coding) regions of the genome, collectively called the exome. While the exome is estimated to comprise ~1.5% of the genome, it contains >80% of recognized disease-causing mutations. Surveying this portion of the genome is therefore an efficient and powerful clinical diagnostic tool for a variety of genetic disorders. Whole exome sequencing at the Center for Personalized Medicine includes analysis of the mitochondrial genome.
In contrast, when the indication for testing is suggestive of a particular type of disorder such as Epidermolysis bullosa, pulmonary arterial hypertension, or a mitochondrial disorder, a focused exome analysis can be performed. Focused exome utilizes a targeted approach whereby only the genes that are associated with a patient’s clinical and family history are analyzed. This provides a genome-wide assessment of all relevant genes that is substantially more efficient than traditional sequential single gene or multi-gene panel testing, with the built-in flexibility to add newly discovered disease genes. The exact genetic diagnosis of these inherited diseases may assist in genetic counseling as well as clinical management of these patients.
Given that this test is driven by clinical and family history of a patient, exact phenotyping is of utmost importance. The clinical team should complete the clinical history form with all pertinent information. In addition, the providers have the option to provide a list of genes that they want to be analyzed. Incidental findings in genes not relevant to a patient’s diagnosis are not analyzed or reported.
Focused exome sequencing is only designed to reliably detect single nucleotide variants (SNVs) and small deletions and insertions (<10 bp) and is not currently validated to reliably detect large (>10 bp) deletions and duplications. If exon level deletion/duplications, mitochondrial depletion, or large mtDNA deletions are suspected, we recommend performing appropriate clinical testing using an alternate methodology.
Oncology Genetic Testing
Working with our colleagues in the Division of Anatomic Pathology, many of whom are internationally recognized authorities in pathologic diagnosis, we are able to combine their analyses with our state-of-the-art molecular genetic and next-generation sequencing-based testing into fully integrated pathology genomic reporting. This combination of state-of-the-art genomic testing and integrated reporting enables clinicians to access all the information they need to create personalized treatment plans for pediatric cancer. In addition to this, our faculty members are internationally recognized for their experience in pediatric cancer predisposition and offer tests to detect genetic predisposition to known cancers, including rhabdoid tumor and retinoblastoma.
- BRAF Sanger Sequencing
- Cancer Predisposition Panel
- Chromosomal Microarray Analysis - Oncology
- OncoKids® Cancer Panel
- RNASeq- Gene Fusion
- Retinoblastoma - RB1 Molecular Genetic Analysis
- SMARCB1 Molecular Genetic Analysis
This BRAF Sanger Sequencing test identifies mutations in exon 15, including the common BRAF V600E mutation. A positive finding helps refine diagnosis and prognosis, and may be used to determine eligibility for biologically targeted therapy. This testing is indicated for individuals with a diagnosis of several cancer types including brain tumors, melanoma, and thyroid cancer. BRAF exon 15 mutations have been reported in a variety of brain tumors including gliomas such as astrocytomas and gangliogliomas; patients with brain tumors harboring these mutations may be eligible for treatment with BRAF inhibitors such as vermurafenib. Approximately fifty percent of melanomas harbor BRAF V600E or V600K mutations. These mutations confer sensitivity to several FDA-approved targeted therapies including BRAF inhibitors (vemurafenib, dabrafenib) and a MEK inhibitor (trametinib) in this disease process. BRAF exon 15 mutations can aid in the diagnosis of thyroid cancer and are seen in one third to one half of papillary thyroid cancers.
This testing should be used for genetic characterization of tumor samples at the time of diagnosis; it is not indicated for tumor surveillance or detection of residual disease, because of its limited sensitivity for low level mosaicism (low percentage of tumor cells in the sample). Acceptable sample types include fresh frozen tumor tissue and formalin fixed tumor samples.
Approximately twenty percent of pediatric patients with hematologic malignancies or solid tumors are genetically predisposed to developing cancer due to a de novo or inherited alteration in their germline DNA. Identification of the underlying nature of this genetic alteration is critical for patient management, including selection of therapy, determining the risk for second primary tumors, and for family counseling.
Our custom Cancer Predisposition Panel (CPP) is comprised of two tiers of genes. Tier 1 genes (279 genes) include well validated autosomal dominant and recessive genes associated with germline cancer risk in both pediatric and adult patients such as TP53, RB1, SMARCB1, BRCA1, BRCA2, NRAS, MLH1, MSH2, MSH6, etc. Tier 2 genes (222 genes) may be associated with cancer predisposition but there is less extensive literature to support the gene-disease association and/or risk estimates. Patient samples will be analyzed for alterations in Tier 1 genes first, and if there is no evidence for a pathogenic alteration, the analysis will be expanded to include Tier 2 genes. A full list of genes in both Tiers is shown below.
The CPP test is a hybrid capture assay developed in collaboration with Twist Bioscience. The test is designed to detect single nucleotide variants (SNVs) and small deletions and insertions (InDels, <10 bp) as well as copy number variants in the panel of 501 genes. The assay yields approximately 800-1000x sequencing coverage, and the limit of detection of this assay is 5% for SNVs and 10% for InDels for regions with the depth of coverage above 100x. Please note that the sensitivity for sequence variant and copy number detection is 97% and 79%, respectively. The decreased sensitivity for copy number alterations is due to the technical limitations in detecting single exon deletions in many of the genes on the panel. Supplemental assays such as multiplex ligation probe amplification (MLPA) or the Xon chromosomal microarray assay may be used to rule out single exon deletions or duplications in the setting of a non-informative CPP result. Similarly, several genes with pseudogenes are difficult to analyze with next generation sequencing-based assays. Specifically, PMS2 copy number variant detection requires additional testing with a companion MLPA assay.
CPP testing should be considered for all patients with a reported family history of cancer, or with phenotypic evidence for a genetic disorder and a malignancy. Similarly, genetic testing with the CPP should be considered following somatic testing of the bone marrow or tumor tissue in a patient with leukemia/lymphoma, or a solid tumor if there is suspicion for an underlying germline variant. Pre-test counseling is required before initiation of testing. Patients with a confirmed alteration in a gene on the CPP will be offered follow-up counseling in the Cancer Predisposition Clinic, directed by Dr. Matthew Deardorff, Director of Personalized Care at CHLA. Testing of related individuals to rule out inheritance of the genetic alteration can be performed by targeted mutation or copy number analysis.
The preferred sample type is peripheral blood, although saliva, buccal swab, skin fibroblast or bone marrow samples will also be accepted. Detailed information about sample requirements can be found in the Lexicomp manual.
Please contact the CPM team at firstname.lastname@example.org for additional details.
Tier 1 gene list:
ACD, AIP, AKT1, ALK, ANKRD26, APC, ARID1A, ARID1B, ARID2, ARID5B, ASXL1, ATM, ATR, ATRX, AXIN2, BAP1, BARD1, BCORL1, BLM, BMPR1A, BRAF, BRCA1, BRCA2, BRIP1, BUB1B, CARD11, CASP10, CBL, CD27, CD70, CDC73, CDH1, CDH23, CDK4, CDKN1B, CDKN1C, CDKN2A, CDKN2B-AS1, CEBPA, CHEK2, CREBBP, CSF3R, CTNNA1, CTR9, CXCR4, CYLD, DDB2, DDX41, DICER1, DIS3L2, DKC1, DNAJC21, DNMT3A, EFL1, EGFR, EGLN1, ELP1, ENG, EPAS1, EPCAM, EPO, ERBB2, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6L2, ETV6, EXT1, EXT2, EZH2, FAH, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAS, FASLG, FBXW7, FGFR1, FH, FLCN, FOXE1, GALNT12, GALNT14, GATA1, GATA2, GFI1, GJB2, GNAQ, GNAS, GPC3, GPC4, GREM1, HAX1, HNF1A, HOXB13, HRAS, IDH1, IDH2, IKZF1, IL7R, ITK, JAGN1, JAK1, JAK2, JMJD1C, KIF1B, KIT, KLHDC8B, KLLN, KMT2A, KRAS, LIG4, LZTR1, MAD2L2, MAP2K1, MAP2K2, MAP3K6, MAX, MBD4, MC1R, MECOM, MEN1, MET, MITF, MLH1, MLH3, MPL, MRE11, MSH2, MSH3, MSH6, MST1R, MTAP, MUTYH, MYB, MYH9, NBN, NF1, NF2, NHP2, NKX2-1, NOP10, NOTCH2, NPAT, NPM1, NRAS, NSD1, NTHL1, PALB2, PALLD, PARN, PAX5, PBRM1, PDGFRA, PDGFRB, PHOX2B, PICALM, PIEZO1, PIK3CA, PIK3CD, PIK3R1, PMS1, PMS2, POLD1, POLE, POLH, POT1, PPM1D, PRF1, PRKAR1A, PTCH1, PTCH2, PTEN, PTPN11, PTPRD, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD54B, RAD54L, RAF1, RASA2, RB1, RECQL, RECQL4, REST, RET, RFWD3, RHBDF2, RIT1, RMRP, RNASEL, ROS1, RPL11, RPL15, RPL26, RPL27, RPL31, RPL35, RPL35A, RPL5, RPS10, RPS15, RPS15A, RPS19, RPS20, RPS24, RPS26, RPS27, RPS28, RPS29, RPS7, RTEL1, RUNX1, SAMD9, SAMD9L, SBDS, SDHA, SDHAF2, SDHB, SDHC, SDHD, SETBP1, SF3B1, SH2B3, SH2D1A, SHOC2, SLC25A11, SLX4, SMAD4, SMARCA4, SMARCB1, SMARCE1, SMO, SOS1, SOS2, SPRED1, SRGAP1, SRP54, SRP72, SRY, STAT3, STK11, SUFU, TERC, TERF2IP, TERT, TET2, TINF2, TMEM127, TP53, TRIP13, TSC1, TSC2, TSR2, UBE2T, UNC13D, USB1, VHL, WIPF1, WRAP53, WRN, WT1, XIAP, XPA, XPC, XRCC2, XRCC4
Tier 2 gene list:
ABCB11, ABCB7, ABCG5, ABCG8, ABRAXAS1, ACACA, ACBD5, ACTN1, ADA, ADA2, AK2, ALAS2, AMN, ANK1, ANO7, AP3B1, ARHGAP11A, ARHGEF12, ARPC1B, ATP7B, BLOC1S3, BLOC1S6, BRD4, BRF1, C15orf41, CAPN9, CDAN1, CIP2A, CLCN7, CLEC12B, CLPB, COL7A1, CPA1, CPB1, CSF2RA, CTC1, CTLA4, CUBN, CYB5R3, CYCS, DCLRE1B, DCLRE1C, DDB1, DDX1, DHFR, DNAH7, DNTT, DOCK8, DROSHA, DTNBP1, DUT, ELANE, EP300, EPB42, EXO1, FEN1, FGFR3, FLI1, FLNA, FYB1, G6PC, G6PC3, G6PD, GALE, GAR1, GBA, GBE1, GFI1B, GINS1, GLRX5, GMPS, GNE, GP1BA, GP1BB, GP9, GPI, GRHL2, GSS, GYS2, HABP2, HBA1, HBA2, HBB, HFE, HMBS, HOXA11, HPS1, HPS3, HPS4, HPS5, HPS6, IFNGR1, IFNGR2, IPMK, ITGA2, ITGA2B, ITGB3, KDM1A, KDM3B, KIF23, KITLG, KLF1, KMT2D, L2HGDH, LAMTOR2, LIG1, LIG3, LPIN2, LYST, MAGT1, MASTL, MCM9, MDC1, MDH2, MKL1, MPIG6B, MTR, MYD88, MYO18B, NAF1, NBEAL2, NHEJ1, NIN, NOTCH3, NSUN2, NT5C3A, OCA2, PARP1, PC, PDHA1, PDHX, PGM3, PKLR, POLA1, POLB, POLDIP2, POLE2, POLQ, PRDM9, PRKACG, PRKDC, PROKR2, PRSS1, PUS1, PZP, RAB27A, RAC2, RBBP6, RBM8A, REN, RETSAT, RHAG, RINT1, RNF31, RPA1, RPL19, RPL23, RPL36, RPS27A, RRAS, SBF2, SEC23B, SEMA4A, SERPINA1, SETD6, SLC19A2, SLC22A16, SLC25A13, SLC25A38, SLC35C1, SLC37A4, SLC45A2, SLC4A1, SLC7A7, SLFN14, SMAD3, SMARCA2, SMARCD2, SPINK1, SPRTN, SPTA1, SPTB, SRC, STAT2, STN1, STX11, STXBP2, TAZ, TCIRG1, TCN2, TEN1, TF, TGFBR1, THBD, THPO, TJP2, TMPRSS6, TNFAIP3, TNFRSF13B, TNFRSF13C, TP53AIP1, TP53BP1, TP63, TPI1, TRIM28, TRIM37, TRNT1, TSHR, TUBB1, TYK2, TYR, TYRP1, ULK4, UNG, UROD, VPS13B, VPS45, WAS, WDR1, XRCC1, XRCC5, YARS2
Chromosomal Microarray Analysis provides a high-resolution, genome-wide assessment of copy number alterations and loss of heterozygosity in DNA isolated from bone marrow samples, leukemic peripheral blood samples, bone and soft tissue tumors and central nervous system tumors. The results are intended for use by the physician to further refine diagnoses, offer more accurate prognostic assessments and select optimal treatments. Fresh and frozen tumor tissue and bone marrow aspirate samples are processed using the CytoScan® HD Array from Affymetrix. DNA isolated from formalin fixed and paraffin embedded specimens (FFPE) is analyzed using the OncoScan® FFPE Array (Affymetrix). Due to the higher resolution of the CytoScan HD array, the analysis of fresh or frozen tissue is recommended.
The OncoKids® cancer panel is a primer-based target enrichment, next-generation sequencing assay designed to detect diagnostic, prognostic and biologic markers for targeted therapy across the spectrum of pediatric cancers. These cancers include leukemias, sarcomas, brain tumors and embryonal tumors. OncoKids® is a targeted gene panel intended to guide the diagnosis and treatment of cancer in pediatric patients based on the genomic alterations specific to their tumor.
OncoKids® Cancer Panel
The DNA content of the OncoKids® panel consists of over 3,000 amplicons and covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes. The RNA content includes over 1,400 targeted gene fusions associated with acute myeloid leukemia, acute lymphoblastic leukemia, childhood sarcomas, pediatric brain tumors and soft tissue tumors.
The assay requires 20 ng of DNA and 20 ng of RNA derived from blood, bone marrow, and fresh, frozen or formalin fixed tumor tissue (FFPE). The assay utilizes highly multiplexed Ion AmpliSeq™ primers and next-generation sequencing technologies to detect somatic variants, high-level gene amplifications and gene fusions. For the DNA component of the assay, the mean read depth is over 3,000x with greater than 90 percent on-target reads. For the RNA component, targeted fusion read counts vary between 1,000x and 100,000x in positive samples. Downstream data analysis utilizes Ion Reporter™ and a proprietary custom software suite for clinical analysis, Integrated Curation Environment (ICE), developed by CHLA’s Center for Personalized Medicine.
The OncoKids® clinical assay was validated by the Children’s Hospital Los Angeles Center for Personalized Medicine, which is certified by the College of American Pathologists under the Clinical Laboratory Improvement Amendments of 1988. The U.S. Food and Drug Administration (FDA) has not approved or cleared this test; however, FDA approval or clearance is currently not required for clinical use of this test. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions. This test should not be regarded as investigational or for research use.
OncoKids® Panel Features
OncoKids® is a comprehensive gene panel developed for children and young adults with leukemia, solid tumors, sarcomas, brain tumors and embryonal tumors.
- Designed specifically for pediatric cancers by pediatric geneticists, oncologists and pathologists
- Developed and validated in a CAP/CLIA environment
- Utilizes 10x less sample material than other next-generation sequencing cancer assays; critical for pediatric patients with smaller tumors
- Incorporates both DNA and RNA to obtain a more detailed picture of a patient’s tumor profile
- Backed by pediatric specialists ready to discuss clinical cases or field any technical or scientific questions
The Department of Pathology and Laboratory Medicine, on behalf of The Center for Personalized Medicine, is pleased to announce the availability of a new RNA sequencing test for the detection of gene fusions – RNASeq- Gene Fusion. This test extends the scope of fusions detected by our OncoKids pan-cancer sequencing panel to include rare, atypical, and novel gene fusions that are not represented in the design of the OncoKids assay. Gene fusions represent important driver alterations in cancer. The detection of gene fusions may be associated with diagnostic, prognostic, and therapeutic clinical utility. The presence of a gene fusion can help to establish or refine a pathologic diagnosis. Additionally, some fusions are present in only a subset of cases of a given tumor type, and their presence may provide clinically relevant prognostic information that may contribute to risk stratification. Finally, certain gene fusions can be directly targeted by specific therapeutic agents.
The RNASeq- Gene Fusion test examines messenger RNAs from all coding (exonic) regions using a hybridization capture-based method from Twist Bioscience to assess the presence of fusion transcripts. Each RNA specimen is sequenced to obtain greater than 50,000,000 unique mapped next-generation sequencing reads. This data is subsequently interrogated for the presence of gene fusions with clinical significance. Novel reported fusions are confirmed by RT-PCR followed by Sanger sequencing as an orthogonal method.
The RNASeq- Gene Fusion test is appropriate for the detection of gene fusions in CNS tumors, non-CNS solid tumors, and hematologic malignancies. OncoKids should be ordered first in cases where gene fusions of interest are covered by the OncoKids test design. The RNASeq- Gene Fusion test should be ordered in cases where the gene fusion(s) of interest are not covered by the OncoKids test design or following a negative OncoKids result in cases with remaining clinical suspicion for a gene fusion.
Submitted specimens should have at least 50% tumor content. This test is not currently validated for the detection of sequence variants, gene expression changes, or intragenic alterations in RNA splicing, including exon skipping events such as MET exon 14 skipping and EGFR variant III (vIII). If these types of variants are suspected, we recommend performing appropriate clinical testing using an alternate methodology.
RNASeq- Gene Fusion can be ordered by an attending physician in KIDS.
Accepted sample types are peripheral blood, bone marrow, frozen tissue, and formalin fixed paraffin embedded (FFPE) tissue. Note that frozen tissue is preferred over FFPE when available. Detailed information about sample requirements can be found in the Lexicomp manual (http://online.lexi.com/lco/action/home).
Please contact the CPM team at email@example.com for additional details.
Retinoblastoma (Rb) is a malignant tumor of the retina that typically occurs in children before the age of 5 years. A genetic predisposition to Rb is associated with a point mutation, a small insertion or deletion, or a structural alteration (most often leading to a deletion of one or more exons) of the RB1 gene in chromosome band 13q14. The mutation or deletion may be inherited from a parent or occur de novo. Germline carriers of the mutation have a 50% risk of transmitting the mutation to their children, which would predispose them to develop retinoblastoma. The RB1 Molecular Genetic Analysis is performed via Multiplex Ligation-Dependent Probe Amplification (MLPA), Sanger sequencing and next-generation sequencing.
Rhabdoid tumors are particularly aggressive pediatric malignancies that primarily develop in infancy and early childhood. They are referred to as atypical teratoid/ rhabdoid tumors (AT/RT) when they arise in the central nervous system and malignant rhabdoid tumor (MRT) when they are found in renal or extra-renal sites. The vast majority of tumors (both AT/RT and MRT) are characterized by loss of function of the SMARCB1/INI1/SNF5/BAF47 gene in chromosome band 22q11.2. SMARCB1 is an invariant member of the SWI/SNF chromatin-remodeling complex of proteins and thus functions in controlling gene transcription. Deletions, duplications and mutations in the SMARCB1 locus have been demonstrated in more than 95% of rhabdoid tumors. Approximately 25% of patients have a germline alteration in the SMARCB1 gene that predisposed them to the development of the tumor(s). In rare cases, mutations may be inherited from an unaffected parent.
Germline mutations in SMARCB1 are also seen in association with schwannomatosis, in which affected individuals develop multiple, benign nerve sheath tumors (schwannomas). In some families, a parent may have one or more schwannomas, and their offspring develop a rhabdoid tumor. SMARCB1 mutations may also been seen in patients with Coffin-Siris or Nicolaides Barristser syndrome, or in patients with isolated developmental delay.
The molecular genetic analysis of SMARCB1 consists of a Multiplex Ligation-Dependent Probe Amplification (MLPA) assay to detect deletions or duplications of one or more of the nine coding exons of the gene and Sanger sequencing to identify sequence alterations. Depending on the indication for testing, the MLPA assay is typically performed first on frozen tissue, followed by an analysis of a peripheral blood specimen of the affected individual. Parental testing is indicated if a child has been found to have a germline mutation or copy number alteration of the locus.