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.

Oncology

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.

Genetic Diseases

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.

Mark Urata, MD, head of the Division of Plastic and Maxillofacial Surgery, specializes in the most complex and difficult craniofacial anomalies in pediatric patients.

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.

Our Tests

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For questions, please contact the Laboratory Service Center at: 877-543-9522 (KIDZLAB).

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

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.

Chromosomal Microarray Analysis

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

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

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.

Clinical Exome Sequencing - Clinical History Form

Clinical Exome Sequencing - Consent Form

Epilepsy Gene Panel

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.

Epilepsy Panel - Gene List

Clinical Exome Sequencing - Clinical History Form

Focused Exome

Exome Sequencingis 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.

Focused Exome Sequencing - Clinical History Form

Ocular Disease Focused Exome

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 300 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 311 nuclear genes. 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.

Ocular Disease Focused Exome - Gene List

VMD4Kids (Vascular Anomalies and Mosaic Disorders)

Vascular anomalies are a heterogeneous group of disorders consisting of abnormalities in blood vessel growth and development. A growing number of types of vascular anomalies have been demonstrated to be caused by genetic mutations that do not occur in all cells of the anomaly, but only a subset, termed as genetic mosaicism. Some of these causative mutations can occur at very low levels and require a very sensitive assay to detect them.

Vascular anomalies, lymphatic malformations, skin pigmentary differences, generalized body overgrowth, cortical brain malformations and focal bone anomalies can each be caused by mutations in a number of different genes. A mutation in some of these genes can cause clinically different effects if the mutation arises in different tissues. For example, some mutations in the gene PIK3CA can cause vascular anomalies, lymphatic malformations, lipomas, skin pigmentary differences or generalized body overgrowth, depending upon the tissue in which the mutation arose.

Gene and mutation-specific therapies, such as MEK inhibitors, MTOR inhibitors and PIK3CA inhibitors have led to the need for accurate and rapid diagnosis of the molecular basis of these disorders.

The VMDKids panel targets the coding region and intron/exon boundaries for 222 genes including genes associated with comprehensive vascular anomalies (107 genes), isolated capillary malformations (25 genes), lymphatic malformations/venous malformations or arteriovenous malformations (55 genes), lymphedema (54 genes), vascular tumors (25 genes), generalized body overgrowth (50 genes), Noonan syndrome (28 genes), skin pigmentary mosaicism and dermal hypoplasia (49 genes), focal sclerotic bone lesions (5 genes), focal cortical dysplasia (30 genes) and Cornelia de Lange syndrome (15 genes). The test has been validated to detect variants at a variant allele frequency of 1%.

A full list of genes is shown below.

Pre-test counseling is required before initiation of testing. Patients with a confirmed alteration demonstrated with VMD4Kids will be offered follow-up counseling in the Vascular Anomalies Clinic, the Genetic Test Assistance and Counseling Clinic or in a clinic with Dr. Matthew Deardorff, Director of Personalized Care at CHLA. Testing of related individuals to assess inheritance of any relevant genetic alteration can be performed by targeted mutation analysis.

Ordering Instructions

CPM VMD4Kids (Vascular and Mosaic Anomalies Panel) can be ordered in KIDS.

Preferred sample types are peripheral blood, frozen or fresh tissue. FFPE samples will also be accepted.

The turn-around time for the test is six weeks from the time the sample is received in the laboratory.

Please contact the CPM team at askcpm@chla.usc.edu for additional details.

Gene List:

ABCC6, ABCC9, ACTB, ACTG1, ACVRL1, ADAMTS3, AFF4, AKT1, AKT2, AKT3, ALG8, AMER1, ANGPT2, ANKRD11, ANTXR1 , ARAF, ARID1A, ASXL1, ATP2A2, ATP2C1, BMPR2 , BRAF, BRD4, BRWD3, CAMTA1, CARD14, CASK, CAV1, CBL, CCBE1, CCDC88A, CCM2, CCND2, CDC42, CDKN1C, CELSR1, CNTNAP2, COL3A1, COX7B, CTNNB1, DCHS1, DEPDC5, DICER1, DNMT3A, DUSP5, EBP, EDA, EED, EGFR, EIF2AK4, ELMO2, ENG, ENPP1, EP300, EPHB2, EPHB4, EZH2, FAT4, FBN1, FGFR1, FGFR2, FGFR3, FLT1, FLT4, FOS, FOSB, FOXC2, FOXF1, FZD6, GATA2, GDF2, GJA1, GJB2, GJC2, GLA, GLI3, GLMN, GNA11, GNA14, GNAQ, GNAS, GPC3, HCCS, HDAC8, HEPACAM, HGF, HRAS, HTR6, IDH1, IDH2, IKBKG, IRS1, ITGA9, JAK2, KAT6B, KCNJ8, KCNK3, KDR, KIF11, KIF7, KITLG, KRAS, KRIT1, KRT1, KRT10, KRT2, LEMD3, LMNA, LZTR1, MAP2K1, MAP2K2, MAP3K3, MAPK1, MAPK3, MED12, MET, MLC1, MLH1, MPI, MSH2, MSH6, MTOR, MVD, MVK, MYC, NAGA, NDUFB11, NEK9, NF1, NF2, NFIA, NFIX, NIPBL, NOD2, NPRL2, NPRL3, NRAS, NRP1, NRP2, NSD1, NSDHL, NSUN2, OFD1, PCDH19, PDCD10, PDGFRB, PHF6, PIEZO1, PIK3CA, PIK3R1, PIK3R2, PLCB4, PLCG1, PMS2, PMVK, PORCN, PPP1CB, PTCH1, PTCH2, PTEN, PTPN11, PTPN14, PTPRB, RAB39B, RAB6B, RAD21, RAF1, RALA, RASA1, RASA2, RHEB, RHOA, RIN2, RIT1, RNF125, RNF135, RRAS, SCN1A, SCN3A, SETD2, SHOC2, SLC2A1, SLC2A10, SLC35A2, SMAD3, SMAD4, SMAD9, SMC1A, SMC3, SMO, SNRK, SOS1, SOS2, SOX18, SPRED1, STAG2, STAMBP, STRADA, STXBP1, SUFU, SUZ12, TBC1D7, TEK, TERT, TFE3, TGFB, TGFBR1, TGFBR2, THSD1, TIE1, TP53, TSC1, TSC2, UPF3B, VEGFC, VHL, ZNF337, ZNHIT3

Whole Genome Sequencing (WGS) for Patients with Genomic Disorders

The clinical utility of exome and genome sequencing for diagnosis of pediatric disease is well established. Early application has been shown to reduce the time to diagnosis, limiting the diagnostic odyssey, and lowering the cost to patients and healthcare systems. Although the diagnostic yield of WGS varies depending upon the disorder(s) tested, it typically ranges from 30-60% in diverse cohorts.  Trio testing (proband and both parents) is the gold standard. It permits the identification of de novo variants and the determination of the parental origin of variants in recessive genes. Testing of related individuals to assess inheritance of any relevant genetic alteration can be performed by subsequent targeted mutation or copy number analysis.

The Center for Personalized Medicine (CPM) WGS assay combines features of exome sequencing and chromosome microarrays into a single test.  This includes identification of pathogenic variants (single base changes and small insertions and deletions) in all protein-coding exons in both the nuclear and mitochondrial genomes as well as gene level Copy Number Variants (CNVs). Future versions of the CPM WGS test will provide expanded analysis to include identification of a wider range of genetic alterations, including deep intronic and regulatory region variants, structural variants such as balanced inversions and translocations, variants in tandem repeat regions, and variants used to determine pharmacogenomic and polygenic risk. Please note that the sequencing depth (coverage) of the genome is approximately 40x, compared to 140x for exome sequencing. The likelihood of detecting mosaic (low level) variants is therefore much greater with the CPM clinical exome sequencing test (CPM-CES).

Similar to CES, the WGS test is a phenotype driven assay, based on a selection of genes associated with the specific features observed in the patient, referred to as the primary gene list.  Clinically significant single nucleotide variants and small insertions or deletions in genes associated with the primary clinical concern(s), secondary findings in American College of Medical Genetics (ACMG)-actionable genes (if opted-in to receive), genome wide deletions greater than 100kb, duplications greater than 500kb and known pathogenic mitochondrial variants are reported using interpretation categories per ACMG Guidelines.

Ordering

The Genetic Test Assistance and Counseling (GTAC) team is available to support counseling, consenting, and ordering. Please contact them prior to ordering WGS or CES to determine the most appropriate assay.

Counseling and Consent

Pre-test genetic counseling is required prior to WGS consent to ensure that individuals fully understand the benefits, risks, and limitations of this test.  Specifically, WGS is designed to identify disease-causing mutations in all genes, including those related to the patient’s features, as well as a secondary list of genes determined by the American College of Medical Genetics to be medically actionable. These secondary genes include cancer predisposition and cardiac disease genes and may not be directly related to the patient’s current medical issue, and may have implications for other family members. The consent process includes a discussion regarding the optional (i.e. Opt-in) reporting and disclosure of medically actionable genes with the family. Post-test genetic counseling should be provided to the family by a genetic counselor or a clinical geneticist to discuss clinically relevant results as well as available interventions and resources.

Ordering

WGS can be ordered by a physician, front-line team member or GTAC Genetic Counselor.
The following options are orderable in KIDS:

1. Whole Genome Sequencing-Trio (WGS Trio)
2. Whole Genome Sequencing-Proband Only (WGS Proband)
3. Whole Genome Sequencing-Duo (WGS Duo)
4. Whole Genome Sequencing-Family Member (WGS Family)

Acceptable sample types  

1. Peripheral blood collected in EDTA (purple/lavender top tube)
2. DNA extracted from blood

Requirements for performing WGS include:

1. A test order for each individual (proband and family members)
2. A signed consent for each individual
3. Clinical history and relevant medical records
4. Approvals:
   • Outpatient: Prior authorization from insurance or patient/family direct payment.
   • Inpatient: Approval by the GTAC Medical Director

Turn-around time

The turn-around time for WGS is similar to exome sequencing, which is 12 weeks until completion of the final report. Expedited testing can be requested for in-patients with approval by the GTAC Medical Director.

Please contact the GTAC team at GTAC@chla.usc.edu or 323-361-5536 (option 1 for providers) for additional details and questions.

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.

Cancer Predisposition Panel

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.

Please contact the CPM team at askcpm@chla.usc.edu 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 - Oncology

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.

LBSeq4Kids (Liquid Biopsy Whole Genome Sequencing for Kids)

LBSeq4Kids is a new liquid biopsy assay that utilizes low passage Whole Genome Sequencing (WGS) of tumor or cell-free DNA (cfDNA) to detect Copy Number Alterations (CNAs) in patients with non-hematologic cancers.

Tumors shed DNA fragments, referred to as circulating tumor DNA (ctDNA), into bodily fluids. The tumor-derived fragments may be present at very low levels in the cell-free DNA and require sensitive and specific bioinformatics methods to detect them. The LBSeq4Kids assay is designed to detect whole chromosome or partial gains or losses and focal amplifications and deletions which are larger than 3Mb. The assay does not have the gene level resolution that is achievable with our current CytoScanHD or OncoScan Chromosomal Microarrays and is not validated to detect loss of heterozygosity. LBSeq4Kids should therefore not be used when the primary tumor or metastatic lesion can be biopsied or resected. The limit of detection for the assay is a ctDNA fraction of at least 10% in the isolated cell-free DNA sample.

The current test is designed to detect CNAs that may provide diagnostic or prognostic information related to the primary malignancy or metastatic disease. LBSeq4Kids utilizes 1) CSF for CNS tumors including but not limited to high and low-grade gliomas, medulloblastoma, embryonal tumors such as atypical teratoid/rhabdoid tumors, glioneuronal tumors and ependymoma 2) blood plasma for solid tumors including sarcomas, renal, hepatic, and germ-cell tumors and 3) aqueous humor of the eye for tumors such as retinoblastoma. Peripheral blood samples from patients with neuroblastoma, as well as peritoneal or pleural fluid from patients with solid tumors, will be accepted. At present, urine is not a validated sample type for this assay.

Please note that constitutional/germline CNAs will also be detected with this assay. Patients should be counseled prior to testing and advised that follow-up studies may be recommended to confirm a possible germline CNA.

Ordering Instructions

CPM LBSeq4Kids (Liquid Biopsy Whole Genome Sequencing for Kids assay) can be ordered in KIDS.

Preferred sample types are peripheral blood, CSF, or aqueous humor of the eye.

Please contact Dr. Jaclyn Biegel (jbiegel@chla.usc.edu) or the CPM team at askcpm@chla.usc.edu for additional details.

Methylation Array Analysis & MGMT Promoter Analysis

DNA methylation of cytosines in CpG sites throughout the genome is a type of epigenetic mark that is ultimately involved in promoting or decreasing gene expression. Specific patterns of methylation have been associated with a variety of tumor types as well as developmental disorders. In the last several years, DNA methylation profiling has emerged as a diagnostic tool to classify tumors, especially central nervous system tumors, based on a combination of preserved developmental and mutation-induced signatures, and pioneering work from the German Cancer Research Network (DKFZ) and University Hospital Heidelberg.

The DNA repair enzyme O⁶-methylguanine-DNA methyltransferase (MGMT) antagonizes the genotoxic effects of alkylating agents. MGMT promoter methylation is the key regulatory mechanism of MGMT gene silencing and predicts a favorable outcome in patients with glioblastoma who are exposed to alkylating agent chemotherapy. Thus, MGMT status is a key biomarker in the context of glioblastoma and has become a parameter for stratification of patients with glioma within clinical trials.

The CPM Methylation Array Analysis & MGMT Promoter Analysis (MAA) assay uses a commercially available Infinium EPIC array from Illumina to interrogate 850,000 specific methylation sites across the genome, and an established classifier from DKFZ, reimplemented locally at the CPM, for analysis. The classifier is based on the random forest algorithm. It compares the methylation profile of a given tumor with that of over 2,800 reference CNS tumors. The output is a classification and prediction score that indicates the resemblance to one of the characterized CNS tumor classes (91 classes in total). In addition, the MGMT promoter methylation status in the sample is determined.

Ordering Instructions

CPM Methylation Array & MGMT Analysis can be ordered by an attending physician in KIDS.

The acceptable sample types include fresh frozen tissue, FFPE, and genomic DNA extracted from fresh frozen tissue or FFPE. Tumor samples being evaluated should contain >=60% tumor cells. Samples with low tumor purity may reduce the sensitivity of the assay. Rare tumor entities that are not represented in the reference cohort may not be appropriately classified. At the current time, this assay is not intended for classification of non-CNS tumors or hematologic malignancies.

Please contact the CPM team at askcpm@chla.usc.edu for additional details.

OncoKids® Cancer Panel

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

Learn more

RNASeq- Gene Fusion

Gene fusions represent important driver alterations in cancer, especially for pediatric sarcomas and hematologic malignancies. The presence of a gene fusion can help establish or refine a pathologic diagnosis and may provide a therapeutic target for treatment. Additionally, some fusions are present in only a subset of cases of a given tumor type, and yet 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 Center for Personalized Medicine RNA sequencing test for the detection of gene fusions – RNASeq- Gene Fusion 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.

The RNASeq- Gene Fusion test examines messenger RNAs from all coding (exonic) regions using a hybridization capture-based method from Twist Bioscience and a novel bioinformatic pipeline 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.

Ordering Instructions

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.

Please contact the CPM team at askcpm@chla.usc.edu for additional details.

Retinoblastoma - RB1 Molecular Genetic Analysis

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.

SMARCB1 Molecular Genetic Analysis

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.