Mockup #5 - Edge Cases

five_edge_cases.py

{
        "reportType": "carrier_couples",
        "reportSubtype": "standard",
        "phiContentCarrierCouples": {
            "maternalPHI": {
                "name": "Rosalind Franklin",
                "dob": "05/01/1981",
                "gender": "Female",
                "mrn": "12344321",
                "invitaeNo": "RQ123456",
                "testedFor": "150 genes",
            },
            "paternalPHI": {
                "name": "Donald Caspar",
                "dob": "05/01/1976",
                "gender": "Male",
                "mrn": "42968551",
                "invitaeNo": "RQ654321",
                "testedFor": "150 genes",
            },
            "summaryNo": "RQ123456-RQ654321",
            "reportDate": "07/10/2018",
            "clinicalTeamOwners": [
                {
                    "firstName": "Michael",
                    "lastName": "Henderson",
                    "isOrderingClinician": True,
                    "showOwnerNameOnReport": True,
                },
                {
                    "firstName": "Zoe",
                    "lastName": "Holzberger",
                    "isOrderingClinician": False,
                    "showOwnerNameOnReport": True,
                },
            ],
        },
        "revisions": [],
        "primaryFindings": {
            "reportResult": "possible_increased_reproductive_risk",
            "summaryLine": [
                {
                    "text": (
                        "This summary combines this couple's Invitae carrier screen results to show their chance of "
                        "having a child with a tested genetic condition (reproductive risk). This couple screened "
                        "negative for all other conditions tested."
                    ),
                    "level": 1,
                }
            ],
            "summaryResults": [
                {
                    "condition": "Gaucher Disease",
                    "gene": "GBA",
                    "invitaeGeneId": "gba",
                    "inheritance": "Autosomal recessive",
                    "maternalCarrierSummary": {
                        "result": "carrier",
                        "variants": ["c1448T>C (p.Leu483Pro)"],
                        "personalRisk": True,
                    },
                    "paternalCarrierSummary": {
                        "result": "not_tested",
                        "variants": [],
                        "personalRisk": False,
                    },
                    "reproductiveRisk": "possible_increased_risk",
                    "riskScore": "Partner testing recommended",
                    "riskScoreFootnoteReferences": [{"script": "1"}],
                },
                {
                    "condition": "Ataxia telangiectasia",
                    "gene": "ATM",
                    "invitaeGeneId": "atm",
                    "inheritance": "Autosomal recessive",
                    "maternalCarrierSummary": {
                        "result": "carrier",
                        "variants": ["3214G>T"],
                        "personalRisk": True,
                    },
                    "paternalCarrierSummary": {
                        "result": "negative",
                        "variants": [],
                        "personalRisk": False,
                    },
                    "reproductiveRisk": "low_risk",
                    "riskScore": "1 in 39,600 (less than 0.01%) chance of a child with this condition",
                    "riskScoreFootnoteReferences": [],
                },
                {
                    "condition": "GJB2-related DFNB1 nonsyndromic hearing loss and deafness",
                    "gene": "GJB2",
                    "invitaeGeneId": "gjb2",
                    "inheritance": "Autosomal recessive",
                    "maternalCarrierSummary": {
                        "result": "carrier",
                        "variants": ["c.109G>A"],
                        "personalRisk": False,
                    },
                    "paternalCarrierSummary": {
                        "result": "negative",
                        "variants": [],
                        "personalRisk": False,
                    },
                    "reproductiveRisk": "low_risk",
                    "riskScore": "1 in 19,600 (less than 0.01%) chance of a child with this condition",
                    "riskScoreFootnoteReferences": [],
                },
                {
                    "condition": "Galactosemia",
                    "gene": "GALT",
                    "invitaeGeneId": "galt",
                    "inheritance": "Autosomal recessive",
                    "maternalCarrierSummary": {
                        "result": "carrier",
                        "variants": ["c.-119_-116del (Duarte variant)"],
                        "personalRisk": False,
                    },
                    "paternalCarrierSummary": {
                        "result": "carrier",
                        "variants": ["c.-119_-116del (Duarte variant)"],
                        "personalRisk": False,
                    },
                    "reproductiveRisk": "low_risk_for_classic_or_mild_disease",
                    "riskScore": "A child who inherits these variants is unlikely to show symptoms",
                    "riskScoreFootnoteReferences": [],
                },
            ],
            "footnotes": [
                {
                    "text": "This result may impact your own health. See your carrier screen report for more information.",
                    "reference": {"icon": "personal_risk_warning"},
                },
                {
                    "text": (
                        "Based on general population frequency, prior to partner testing, the chance to have a child "
                        "with Gaucher disease is 1 in 632. If the partner screens positive, the chance is increased to 1 "
                        "in 4 (25%). If the partner screens negative, the chance is decreased to 1 in 2244. These risks may "
                        "vary by ethnicity."
                    ),
                    "reference": {"script": "1"},
                },
            ],
        },
        "nextSteps": {
            "comments": [
                {
                    "text": (
                        "See your individual carrier screen report on the following pages for additional information, "
                        "including disease descriptions and ethnicity-specific residual risks."
                    ),
                    "level": 1,
                },
                {
                    "text": (
                        "Consult with a genetic counselor or health care provider to further understand these results and how "
                        "they may vary based on ethnicity, assess family history, and review reproductive options."
                    ),
                    "level": 1,
                },
                {
                    "text": (
                        "To access Invitae's complimentary genetic counseling services, educational resources, and online "
                        "results, register your test at https://www.invitae.com/patients."
                    ),
                    "level": 1,
                },
                {
                    "text": (
                        "Consider sharing individual carrier results with family members because they may be carriers for "
                        "the same condition(s)."
                    ),
                    "level": 1,
                },
                {
                    "text": (
                        "Knowledge of genetic information will improve over time, and new information may impact the risk "
                        "assessment in this summary. Contact Invitae for an updated summary at any time, such as when planning "
                        "for a future pregnancy."
                    ),
                    "level": 1,
                },
            ]
        },
        "additionalInformation": [
            {
                "text": (
                    "This reproductive risk summary combines this couple's individual carrier results to show their "
                    "chance of having a child with a genetic condition (reproductive risk). This assessment is based "
                    "solely on carrier screen(s) performed at Invitae. Carrier screening evaluates the risk of specific "
                    "genetic conditions but does not test for all possible genetic conditions or birth defects. This "
                    "summary lists all conditions one or both members of the couple are carriers for. For conditions that "
                    "screened negative, there remains a small risk that the individual could still be a carrier (residual "
                    "risk). Any quoted reproductive risks apply to each pregnancy, use general population risk numbers, and "
                    "presume no family history of the condition. These risks may vary by ethnicity. This summary is not "
                    "intended to replace the individuals carrier report, which contains additional information including "
                    "all the conditions screened, disease descriptions and ethnicity-specific residual risks. The RQ# of "
                    "each individual's carrier report is listed in the header of this summary."
                ),
                "level": 1,
            }
        ],
        "primaryLabAddress": "1400 16th Street, San Francisco, CA 94103",
}