TOP ralentiza la consulta

SELECT  TOP 1000
        *
FROM    (
        SELECT  patientId, labId, result,
                DENSE_RANK() OVER (PARTITION BY patientId, labId ORDER BY labDate DESC) dr
        FROM    labs
        ) q
PIVOT   (
        MIN(result)
        FOR
        labId IN ([1],[2],[3],[4],[5],[7],[8],[9],[10],[11],[12],[13],[14],[15],[16],[17])
        ) p
WHERE   dr = 1
ORDER BY
        patientId

También puede intentar crear una vista indexada como esta:

CREATE VIEW
        v_labs_patient_lab
WITH SCHEMABINDING
AS
SELECT  patientId, labId, COUNT_BIG(*) AS cnt
FROM    dbo.labs
GROUP BY
        patientId, labId

CREATE UNIQUE CLUSTERED INDEX
        ux_labs_patient_lab
ON      v_labs_patient_lab (patientId, labId)

y utilícelo en la consulta:

SELECT  TOP 1000
        *
FROM    (
        SELECT  lr.patientId, lr.labId, lr.result
        FROM    v_labs_patient_lab vl
        CROSS APPLY
                (
                SELECT TOP 1 WITH TIES
                       result
                FROM   labs l
                WHERE  l.patientId = vl.patientId
                       AND l.labId = vl.labId
                ORDER BY
                       l.labDate DESC
                ) lr
        ) q
PIVOT   (
        MIN(result)
        FOR
        labId IN ([1],[2],[3],[4],[5],[7],[8],[9],[10],[11],[12],[13],[14],[15],[16],[17])
        ) p
ORDER BY
        patientId