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Oxford Desk Reference
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Table of Contents

Introduction Adoption Approach to the consultation with a child with dysmorphism, congenital malformation or developmental delay Autosomal dominant (AD) inheritance Autosomal recessive (AR) inheritance Communication skills Complex inheritance Confidentiality Confirmation of diagnosis Consent for genetic testing Genetic basis of cancer Genetic code and mutations Genomes and genomic variation Genomic imprinting Genomic sequencing and interpretation of data from WES or WGS analyses Mitochondrial inheritance Reproductive options Testing for genetic status Timing and origin of new dominant mutations Useful resources X-linked dominant (XLD), semi-dominant, pseudoautosomal and male sparing inheritance X-linked recessive inheritance Clinical Approach Ambiguous genitalia (including sex reversal) Anal anomalies (atresia, stenosis) Anterior segment eye malformations Arthrogryposis Ataxic adult Ataxic child Brachydactyly Broad thumbs Cardiomyopathy in children under 10 years Cataract Cerebellar anomalies Cerebral palsy Chondrodysplasia punctata Cleft lip and palate Coarse facial features Coloboma Congenital heart disease Congenital hypothyroidism Corneal clouding Deafness in early childhood Developmental delay in the child with consanguineous parents Developmental regression Duane retraction syndrome Dysmorphic child Dystonia Ear anomalies Facial asymmetry Failure to thrive Floppy infant Fractures Generalized disorders of skin pigmentation (including albinism) Hemihypertrophy and limb asymmetry Holoprosencephaly Hydrocephalus Hypermobile joints Hypoglycaemia in the neonate and infant Hypospadias Intellectual disability Intellectual disability with apparent X-linked inheritance Increased bone density Intracranial calcification Large fontanelle Laterality disorders including heterotaxy and isomerism Leukodystrophy/leukoencephalopathy Limb reduction defects Lissencephaly, polymicrogyria and neuronal migration disorders Lumps and bumps Macrocephaly Microcephaly Micrognathia and Robin sequence Microphthalmia and anophthalmia Minor congenital anomalies Nasal anomalies Neonatal encephalopathy and intractable seizures Nystagmus Obesity with and without developmental delay Ocular hypertelorism Oedema generalized or puffy extremeties Oesophageal and intestinal atresia (including tracheo-oesophageal fistula) Optic nerve hypoplasia Overgrowth Patchy hypo- or de-pigmented skin lesions Patchy pigmented skin lesions (including cafe-au-lait spots) Plagiocephaly and abnormalities of skull shape Polydactyly Prolonged neonatal jaundice and jaundice in infants below 6 months Ptosis, blepharophimosis and other eyelid anomalies Radial ray defects and thumb hypoplasia Retinal dysplasia Retinal receptor dystrophies Scalp defects Seizures with developmental delay/intellectual disability Short stature Skeletal dysplasias Structural intracranial anomalies (agenesis of the corpus callosum, septo-optic dysplasia and arachnoid cysts) Sudden cardiac death Suspected non-accidental injury Syndactyly (other than 2-3 toe syndactyly) Unusual hair, teeth, nails and skin Common consultations Achondroplasia Alpha1-antitrypsin deficiency Alport syndrome Androgen insensitivity syndrome (AIS) Angelman syndrome Autism and autism spectrum disorders Autosomal dominant polycystic kidney disease (ADPKD) Beckwith-Wiedemann syndrome (BWS) Charcot-Marie-Tooth disorder (CMT) Ciliopathies Congenital adrenal hyperplasia (CAH) Consanguinity Craniosynostosis Cystic fibrosis (CF) Dementia early onset and familial forms Diabetes mellitus Dilated cardiomyopathy (DCM) DNA repair defects Duchenne and Becker muscular dystrophy (DMD and BMD) Ehlers-Danlos syndrome Epilepsy in infants and children Epilepsy in adults Fascioscapulo-humeral muscular dystrophy (FSHD) Fragile X syndrome (FRAX) Glaucoma Haemochromatosis Haemoglobinopathies Haemophilia and other inherited coagulation disorders Hereditary haemorrhagic telangiectasia (HHT) Herediatry spastic paraplegia (HSP) Hirschprung disease Huntington disease (HD) Hyperlipidaemias Hypertrophic cardiomyopathy (HCM) Immunodeficiency and recurrent infection Incest Leigh encephalopathy Limb-girdle muscular dystrophies Long QT and Brugada syndromes Marfan syndrome Mitochondrial DNA diseases Myotonic dystrophy (DM1) Neural tube defects Neurofibromatosis type 1 (NF1) Noonan syndrome and the RAS-MAPK pathway disorders Parkinson disease Retinitis pigmentosa (RP) Rett syndrome Sensitivity to anaesthetic agents Spinal muscular atrophy (SMA) Stickler syndrome Thrombophilia Tuberous sclerosis (TSC) X-linked adrenoleukodystrophy (X-ALD) Cancer BRCA1 and BRCA2 Breast cancer Cancer surveillance methods Colorectal cancer (CRC) Confirmation of diagnosis of cancer Cowden syndrome (CS) Familial Adenomatous Polyposis (FAP) and adenomatous polyposis (due to MUTYH, NTHL1, POLE & POLD1) Gastric cancer Gorlin syndrome Juvenile polyposis syndrome (JPS) Lynch syndrome Lifestyle factors in cancer: smoking, alcohol, obesity, diet and exercise Li-Fraumini syndrome (LFS) Multiple endocrine neoplasia (MEN) Neurofibromatosis type 2 (NF2) Ovarian cancer Peutz-Jeghers syndrome (PJS) Phaeochromocytoma and Paraganglioma Prostate cancer Renal cancer Retinoblastoma von Hippel-Lindau (VHL) disease Wilms tumour Chromosomes 22q11 deletion syndrome 47,XXX 47,XXY 47,XYY Autosomal reciprocal tranlsocations background Autosomal reciprocal translocations familial Autosomal reciprocal translocations postnatal Autosomal reciprocal translocations prenatal Cell division mitosis, meiosis and non-disjunction Chromosomal mosaicism postnatal Chromosomal mosaicism prenatal Deletions and duplications (including microdeletions and microduplications) Down syndrome (trisomy 21) Edwards syndrome (trisomy 18) Inversions Mosaic trisomy 8 Mosaic trisomy 16 Patau syndrome (trisomy 13) Prenatal diagnosis of sex chromosome aneuploidy Ring chromosomes Robertsonian translocations Sex chromosome mosaicism Supernumerary marker chromosomes (SMCs) postnatal Supernumerary marker chromosomes (SMCs) prenatal Triploidy (69,XXX, 69XXY or 69,XYY) Turner syndrome, 45,X and variants X-autosome translocations Pregnancy and fertility Anterior abdominal wall defects Assisted reproductive technology: in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI) and pre-implantation genetic diagnosis (PGD) Bowed limbs Congenital cystic lung lesions, Currarino syndrome, and sacrococcygeal teratoma Congenital diaphragmatic hernia Cytomegalovirus (CMV) Drugs in pregnancy Female infertility and amenorrhoea: genetic aspects Fetal alcohol syndrome (FAS) Fetal anticonvulsant syndrome (FACS) Fetal akinesia Fetomaternal alloimmunisation (rhesus D and thrombocytopaenia) Hyperechogenic bowel Hyoplastic left heart Imaging in prenatal diagnosis Invasive techniques and genetic tests in prenatal diagnosis Low maternal serum oestriol Male infertility: genetic aspects Maternal age Maternal diabetes mellitus and diabetic embryopathy Maternal phenylketonuria (PKU) Miscarriage and recurrent miscarriage Neonatal (newborn) screening (NS) Non-invasive prenatal diagnosis/testing (NIPD/T) Oedema increased nuchal translucency, cystic hygroma and hydrops Oligohydramnios (Including Potter/ Oligohydramnios sequence) Paternal age Polyhydramnios Posterior fossa malformations Premature ovarian failure (POF) Radiation exposure, chemotherapy, and landfill site Rubella Short limbs Talipes (Club foot) Toxoplasmosis Twins and twinning Urinary tract and renal anomalies (Congenital anomalies of the kidney and urinary tract - CAKUT) Varicella Ventriculomegaly Appendix Antenatal and neonatal screening timelines Bayes theorem Carrier frequency and carrier testing for autosomal recessive disorders Centile charts for boys height and weight Centile charts for girls height and weight Centile charts for occipital-frontal circumference (OFC) CK (Creatine kinase) levels in carriers of Duchenne muscular dystrophy (DMD) Conversion charts from English to metric units for height and weight Denver Developmental Screening Test Distribution of muscle weakness in different types of muscular dystrophy Dysmorphology examination checklist Embryonic fetal development (overview) Family tree sheet and symbols Haploid autosomal lengths of human chromosomes Investigation of lethal metabolic disorder or skeletal dysplasia ISCN Nomenclature Karyotypes Normal range of aortic root dimensions Paternity testing Patterns of cancer Radiological investigations including magnetic resonance imaging (MRI) Skeletal dysplasia charts Staging of puberty

About the Author

Dr Helen Firth, DM FRCP DCH is a Consultant Clinical Geneticist at Cambridge University Hospitals, an Honorary Faculty Member of the Wellcome Trust Sanger Institute, and a Bye-Fellow of Newnham College, Cambridge. Her main research interests are in mapping the clinical genome and the matching of rare genomic variants to empower discovery and diagnosis in rare disease. In 2004, she initiated the DECIPHER project (http://decipher.sanger.ac.uk) that enables clinicians and scientists around the world to share information about rare genomic variants to facilitate diagnosis and help to elucidate the role of genes whose function is not yet known. In 2010 Dr Firth became Clinical Lead for the Deciphering Developmental Disorders study (DDD study) (http://www.ddduk.org), one of the world's largest nationwide, genome-wide sequencing projects in rare disease. The study aims to improve diagnosis and further understanding of the genomic architecture of severe developmental disorders. Dr Jane Hurst is a clinician working full time as a clinical geneticist in the one of the leading children's hospitals in the world; a centre of excellence for the diagnosis and treatment of rare diseases. She moved to her current post in 2010 to lead the dysmorphology service after 18 years working in Oxford, UK. Although primarily a patient-focussed clinician, she has always worked closely with scientific colleagues by identifying families that give important clues to the genetic aetiology. Thus early in her career she identified the first family shown to have leptin deficiency and the two families that led to the cloning of the FOXP2 gene.

Reviews

`Review from previous edition It is very refreshing to review a book written for clinicians by clinicians, which is in a format that reflects situations actually encountered in practice. Information provided by the referring doctor to a clinical geneticist or other specialist before a clinic or ward consultation is usually limited. This new text takes common referral indications and, in a standardized format that manages to be brief and clear without skimping on detail, reminds the clinician of diagnostic possibilities and strategies for investigation and management. This will allow the best possible use to be made of an individual consultation by both the patient and the doctor.' Dian Donnai, Professor of Medical Genetics, University of Manchester, Consultant Clinical Geneticist, Regional Genetics Service, St Mary's Hospital, Manchester, UK `I have been impressed with the thoughtfulness of the topics. This should be a great help to many people who are part of the clinical genetics team....There are up-to-date summaries for the staff member who needs a refresher, as well as the glossary and the headings on fundamental topics, like AD inheritance, for those just starting out. ' Lewis B. Holmes Professor of Pediatrics, Harvard Medical School and Chief, Genetics and Teratology Unit, Massachusetts General Hospital for Children, Boston, Massachusetts, USA `This is going to be an extremely useful reference source. The authors have done an outstanding job of summarizing, in one or two pages, pertinent recommendations regarding diagnoses and management of specific disorders as well as practical approaches to a variety of problems that commonly present in real life. ' Marilyn Jones, Adjunct Professor of Pediatrics, University of California, San Diego and Director, Dysmorphology and Genetics, Children's Hospital San Diego, USA `...a comprehensive and highly focussed guide to clinical genetics that should certainly rank as an indeispensable handbook for consultants in clinical genetics, genetic counsellors and paediatricians. However, it should also be extremely useful for PhD students in nearly all disciplines within medical and/or human genetics. Its major strength is the well-conceived and clearly laid out format which enables the reader to obtain a rapid yet quite substantial overview of a plethora of difficult topics...' Human Genetics `The authors of [this book] deserve to be congratulated for achieving the impossible...Overall this book is a winner and is a must for every clinical genetics department. This is arguably the most important book ever published for trainees in genetics...[but] can be considered as an extremely useful reference source to any genetics physician...this book is a 'peripheral brain' and 'lifesaver' for geneticists in many situations!' Ulster Medical Journal Vol 75, no 3 `If there was a Booker Prize for new texts on clinical genetics, then the winner this year would be a foregone conclusion. No one else could possibly come up with and entry as good as this. ... the definitive hands-on guide to clinical genetics. ... The breadth and depth of information provided is remarkable. ... As a practical guide to the specialty of clinical genetics this book has no match, and overall it represents an awesome achievement. How did the authors manage to acquire and collate all this knowledge? Where did they find all this information? ... If your department can only afford one book this year, make it this one. Better still, buy your own copy and keep it hidden because it is going to be much in demand.' BMJ `This is an amazing compilation of genetic knowledge. It provides a fantastic tool for clinical geneticists who require a fast review of specific genetic subjects while performing clinical consultations. ... Condensation of the amount of information included in this wonderful book could not be done any better. ... This is a most-have tool for all clinical geneticists who require quick and specific reviews in clinical practice. ... Dr Firth and Hurst have achieved a tremendous goal. They have been able to summarize a tremendous amount of information in clinical genetics and convert it to an excellent tool for the practice of the specialty. It could not be done any better. The magnificent work done suggests that as the field of clinical genetics expands, further editions will be needed. This is a must have book, and a second edition would be expected.' Doody's Journal

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